Reagents for the Detection of Protein Phosphorylation in ATM &amp; ATR Kinase Signaling Pathways

ABSTRACT

The invention discloses nearly 300 novel phosphorylation sites identified in signal transduction proteins and pathways underlying human ATM/ATR kinase signaling pathways, and provides phosphorylation-site specific antibodies and heavy-isotope labeled peptides (AQUA peptides) for the selective detection, profiling and quantification of these phosphorylated sites/proteins, as well as methods of using the reagents for such purpose. Among the phosphorylation sites identified are sites occurring in the following protein types: DNA repair proteins, Adaptor/Scaffold proteins, Cell cycle regulation proteins, G Protein/GTPase Activating/Guanine Nucleotide Exchange Factor proteins, DNA binding proteins, DNA replication proteins, Kinases, Disease associated proteins proteins, Methyltransferase, Ubiquitin conjugating proteins, Proteases, Phosphatases, and Transcription proteins.

RELATED APPLICATIONS

This application claims the benefit of, and priority to, U.S. Ser. No. 60/795,440, filed Apr. 27, 2006, presently pending, the disclosure of which is incorporated herein, in its entirety, by reference

FIELD OF THE INVENTION

The invention relates generally to antibodies and peptide reagents for the detection of protein phosphorylation, and to protein phosphorylation in cancer.

BACKGROUND OF THE INVENTION

The activation of proteins by post-translational modification is an important cellular mechanism for regulating most aspects of biological organization and control, including growth, development, homeostasis, and cellular communication. Protein phosphorylation, for example, plays a critical role in the etiology of many pathological conditions and diseases, including cancer, developmental disorders, autoimmune diseases, and diabetes. Yet, in spite of the importance of protein modification, it is not yet well understood at the molecular level, due to the extraordinary complexity of signaling pathways, and the slow development of technology necessary to unravel it.

Protein phosphorylation on a proteome-wide scale is extremely complex as a result of three factors: the large number of modifying proteins, e.g. kinases, encoded in the genome, the much larger number of sites on substrate proteins that are modified by these enzymes, and the dynamic nature of protein expression during growth, development, disease states, and aging. The human genome, for example, encodes over 520 different protein kinases, making them the most abundant class of enzymes known. See Hunter, Nature 411: 355-65 (2001). Most kinases phosphorylate many different substrate proteins, at distinct threonine, serine, and/or threonine residues. Indeed, it is estimated that one-third of all proteins encoded by the human genome are phosphorylated, and many are phosphorylated at multiple sites by different kinases. See Graves et al., Pharmacol. Ther. 82:111-21 (1999).

Many of these phosphorylation sites regulate critical biological processes and may prove to be important diagnostic or therapeutic targets for molecular medicine. For example, of the more than 100 dominant oncogenes identified to date, 46 are protein kinases. See Hunter, supra. Understanding which proteins are modified by these kinases will greatly expand our understanding of the molecular mechanisms underlying oncogenic transformation. Therefore, the identification of, and ability to detect, phosphorylation sites on a wide variety of cellular proteins is crucially important to understanding the key signaling proteins and pathways implicated in the progression of diseases like cancer.

Such pathways include the ability of a non-cancerous cell to stop progression through the cell cycle in response to genomic defects is termed the DNA damage checkpoint. See Hartwell et al., Science, 246(4930): 629-34 (1989). It is thought that activation of these checkpoint mechanisms allows time for cells to repair or bypass DNA damage without potentially lethal entry into mitosis.

Central to the proper function of the DNA damage checkpoint are the phosphoinositol 3 phosphate kinase (PI3K) like kinases, ataxia telangiectasia mutated (ATM), ATM and Rad3 related (ATR), DNA dependent protein kinase (DNA-PK), and the more recently discovered member of the family, SMG1. See Abraham et al., Genes Dev. 15:2177-2196 (2001). In response to DNA damage, these kinases are activated (through as of yet undetermined mechanisms), leading to activation of signaling pathways that (1) block progression through the cell cycle, (2) coordinate repair activities, and (3) affect transcription of DNA damage response genes. It is has been shown that ATM is activated by the presence of double stranded breaks (DSBs) in the genome, such as those generated by gamma irradiation (IR). See Banin et al., Science, 281(5383): 1674-7. (1998). In contrast, ATR is activated by a variety of genotoxic agents, such as UV light, alkylating agents, and perturbation of DNA replication by inhibitors such as aphidicolin and hydroxyurea. See Cliby et al., EMBO J., 17(1): 159-69. (1998). It has also been demonstrated that ATR has a role in normal cell cycle progression, as ATR deletion results in embryonic lethality. See de Klein et al., Curr Biol. 10(8):479-82. (2000). The role of DNA-PK is less clear, though it is known to be involved in the response to both DSBs and UV damage of DNA. See Park et al., J Biol. Chem., 274 (45):32520-7 (1999).

Once activated and/or localized, various adaptor proteins control the activities of ATM/ATR/DNA-PK. In the case of ATR, the adaptor ATRIP has been shown to be important not only for proper localization of ATR in response to damage, but also for signaling to downstream targets. Like ATR, an adaptor also controls ATM localization and activity. In this case the adaptor is the aforementioned heterotrimeric complex of Mre11, NBS1, and Rad50 (M/R/N). This complex has been shown to localize to sites of Double Strand Breaks (DSB's) early in the damage response, and is thought to be important in activating ATM at sites of damage. Proper function of DNA-PK has similarly been shown to depend on another adaptor complex made up of the Ku proteins. See Cortez et al., 2001, Falck et al., 2005, Lee and Paul, 2005).

Many effects of ATM and ATR are mediated by their so-called effector kinases, Chk1 for ATR, and Chk2 for ATM. See Guo et al., Genes Dev. 14(21): 2745-56. (2000). ATR or ATM activates these kinases through phosphorylation in response to damage, and they subsequently carry out some of the best-characterized functions of the DNA damage checkpoint. As adaptor proteins regulate ATM/ATR, the functions of Chk1, and possibly of Chk2, also appear to be regulated by adaptors. The protein Claspin, for example, has been shown to be necessary for the ATR-dependent phosphorylation and activation of Chk1. See Kumagai et al., J. Cell Biol. 142:1559-69 (2001). There is currently no known adaptor for Chk2, however, some have speculated that BRCA1 may fulfill this role. See Cortez et al., Science, 294(5547):1713-6 (1999).

Although the best-characterized pathways of the DNA damage checkpoint rely on the action of the effector kinases, Chk1 or Chk2, it is clear that ATM/ATR/DNA-PK target other DNA damage response proteins independently. Other examples of known ATM/ATR substrates include BRCA1, p95/NBS1, MDM2, CtIP, 4E-BP1, SMC1, H2AX, and 53BP1. See Kastan et al., Mol Cell Biol., 1(3):179-86 (2000). In more general terms, it has been shown that the PI3K-like family of kinases has a substrate preference for serine or threonine with a glutamine at the +1 position (the S/TQ motif). Additionally, positively charged residues surrounding the S/T-Q motif inhibit efficient substrate phosphorylation by ATM/ATR (Kim, 1999, O'Neill et al., 2000). New substrates of the PI3K-like kinases are continually being discovered, although the discovery process has to date been laborious, finding only one or a few new substrates at a time.

Despite the identification of a few key molecules involved in ATM and ATR protein kinase signaling pathways, the vast majority of signaling protein changes underlying these pathways remains unknown. There is, therefore, relatively scarce information about kinase-driven signaling pathways and phosphorylation sites relevant to ATM and ATR. This has hampered a complete and accurate understanding of how protein activation within signaling pathways may be driving the malfunction of the DNA damage checkpoint and cancer.

Accordingly, there is a continuing and pressing need to unravel the molecular mechanisms of ATM/ATR kinase-driven oncogenesis in cancer by identifying the downstream signaling proteins mediating cellular transformation. Identifying particular phosphorylation sites on such signaling proteins and providing new reagents, such as phospho-specific antibodies and AQUA peptides, to detect and quantify them remains particularly important to advancing our understanding of the biology of this pathway. Moreover, identification of downstream signaling molecules and phosphorylation sites involved in ATM/ATR signaling and development of new reagents to detect and quantify these sites and proteins may lead to improved diagnostic/prognostic markers, as well as novel drug targets, for the detection and treatment of cancer.

SUMMARY OF THE INVENTION

The invention discloses nearly 300 novel phosphorylation sites identified in signal transduction proteins and pathways relevant to ataxia telangiectasia mutated (ATM) and ATM Rad3 related (ATR) kinase signaling and provides new reagents, including phosphorylation-site specific antibodies and AQUA peptides, for the selective detection and quantification of these phosphorylated sites/proteins. Also provided are methods of using the reagents of the invention for the detection, profiling and quantification of the disclosed phosphorylation sites.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1—Is a diagram broadly depicting the immunoaffinity isolation and mass-spectrometric characterization methodology (IAP) employed to identify the novel phosphorylation sites disclosed herein.

FIG. 2—Is a table (corresponding to Table 1) enumerating the ATM and/or ATR signaling protein phosphorylation sites disclosed herein: Column A=the name of the parent protein; Column B=the SwissProt accession number for the protein (human sequence); Column C=the protein type/classification; Column D=the threonine or serine residue (in the parent protein amino acid sequence) at which phosphorylation occurs within the phosphorylation site; Column E=the phosphorylation site sequence encompassing the phosphorylatable residue (residue at which phosphorylation occurs (and corresponding to the respective entry in Column D) appears in lowercase; Column F=the type of disease in which the phosphorylation site was discovered; and Column G=the cell type(s) in which the phosphorylation site was discovered.

FIG. 3—is an exemplary mass spectrograph depicting the detection of the serine 395 phosphorylation site in NuMA-1 (see Row 40 in FIG. 2/Table 1), as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); S* indicates the phosphorylated serine (shown as lowercase “s” in FIG. 2).

FIG. 4—is an exemplary mass spectrograph depicting the detection of the threonine 286 phosphorylation site in NLK (see Row 173 in FIG. 2/Table 1), as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); T* indicates the phosphorylated threonine (shown as lowercase “t” in FIG. 2).

FIG. 5—is an exemplary mass spectrograph depicting the detection of the serine 352 phosphorylation site in Bcl-9 (see Row 58 in FIG. 2/Table 1), as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); S* indicates the phosphorylated serine (shown as lowercase “s” in FIG. 2).

FIG. 6—is an exemplary mass spectrograph depicting the detection of the serine 951 phosphorylation site in Smc1 (see Row 111 in FIG. 2/Table 1), as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); S* indicates the phosphorylated serine (shown as lowercase “s” in FIG. 2).

FIG. 7—is an exemplary mass spectrograph depicting the detection of the serine 161, 164 and 172 phosphorylation sites in FOXJ2 (see Rows 224-226 in FIG. 2/Table 1), as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); S* indicates the phosphorylated serine (shown as lowercase “s” in FIG. 2).

DETAILED DESCRIPTION OF THE INVENTION

In accordance with the present invention, nearly 300 novel protein phosphorylation sites in signaling proteins and pathways underlying ATM and ATR kinase signaling have now been discovered. These newly described phosphorylation sites were identified by employing the techniques described in “Immunoaffinity Isolation of Modified Peptides From Complex Mixtures,” U.S. Patent Publication No. 20030044848, Rush et al., using cellular extracts from a variety of glioblastoma-derived cell lines, e.g. M059K, 293T etc., as further described below. The novel phosphorylation sites (threonine or serine), and their corresponding parent proteins, disclosed herein are listed in Table 1. These phosphorylation sites correspond to numerous different parent proteins (the full sequences of which (human) are all publicly available in SwissProt database and their Accession numbers listed in Column B of Table 1/FIG. 2), each of which fall into discrete protein type groups, for example DNA repair proteins, Protein Kinases, and Vesicle proteins, etc. (see Column C of Table 1), the phosphorylation of which is relevant to signal transduction activity underlying ATM and ATR kinase signaling, as disclosed herein.

The discovery of the nearly 300 novel protein phosphorylation sites described herein enables the production, by standard methods, of new reagents, such as phosphorylation site-specific antibodies and AQUA peptides (heavy-isotope labeled peptides), capable of specifically detecting and/or quantifying these phosphorylated sites/proteins. Such reagents are highly useful, inter alia, for studying signal transduction events underlying the progression of cancer. Accordingly, the invention provides novel reagents—phospho-specific antibodies and AQUA peptides—for the specific detection and/or quantification of as ATM and/or ATR kinase signaling protein/polypeptide only when phosphorylated (or only when not phosphorylated) at a particular phosphorylation site disclosed herein. The invention also provides methods of detecting and/or quantifying one or more phosphorylated ATM and/or ATR kinase signaling proteins using the phosphorylation-site specific antibodies and AQUA peptides of the invention and methods of obtaining a phosphorylation profile of such proteins (e.g. Kinases).

In part, the invention provides an isolated phosphorylation site-specific antibody that specifically binds a given ATM and/or ATR kinase signaling protein only when phosphorylated (or not phosphorylated, respectively) at a particular threonine or serine enumerated in Column D of Table 1/FIG. 2 comprised within the phosphorylatable peptide site sequence enumerated in corresponding Column E. In further part, the invention provides a heavy-isotope labeled peptide (AQUA peptide) for the detection and quantification of a given ATM and/or ATR kinase signaling protein, the labeled peptide comprising a particular phosphorylatable peptide site/sequence enumerated in Column E of Table 1/FIG. 2 herein. For example, among the reagents provided by the invention is an isolated phosphorylation site-specific antibody that specifically binds the ILF2 transcription protein only when phosphorylated (or only when not phosphorylated) at threonine 388 (see Row 254 (and Columns D and E) of Table 1/FIG. 2). By way of further example, among the group of reagents provided by the invention is an AQUA peptide for the quantification of phosphorylated ILF2 transcription protein, the AQUA peptide comprising the phosphorylatable peptide sequence listed in Column E, Row 254, of Table 1/FIG. 2 (which encompasses the phosphorylatable threonine at position 388).

In one embodiment, the invention provides an isolated phosphorylation site-specific antibody that specifically binds a human ATM and/or ATR kinase signaling protein selected from Column A of Table 1 (Rows 2-301) only when phosphorylated at the threonine or serine residue listed in corresponding Column D of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E of Table 1 (SEQ ID NOs: 1-300), wherein said antibody does not bind said signaling protein when not phosphorylated at said threonine or serine. In another embodiment, the invention provides an isolated phosphorylation site-specific antibody that specifically binds an ATM and/or ATR kinase signaling protein selected from Column A of Table 1 only when not phosphorylated at the threonine or serine residue listed in corresponding Column D of Table 1, comprised within the peptide sequence listed in corresponding Column E of Table 1 (SEQ ID NOs: 1-300), wherein said antibody does not bind said signaling protein when phosphorylated at said threonine or serine. Such reagents enable the specific detection of phosphorylation (or non-phosphorylation) of a novel phosphorylatable site disclosed herein. The invention further provides immortalized cell lines producing such antibodies. In one preferred embodiment, the immortalized cell line is a rabbit or mouse hybridoma.

In another embodiment, the invention provides a heavy-isotope labeled peptide (AQUA peptide) for the quantification of an ATM and/or ATR kinase signaling protein selected from Column A of Table 1, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E of Table 1 (SEQ ID NOs: 1-300), which sequence comprises the phosphorylatable threonine or serine listed in corresponding Column D of Table 1. In certain preferred embodiments, the phosphorylatable threonine or serine within the labeled peptide is phosphorylated, while in other preferred embodiments, the phosphorylatable residue within the labeled peptide is not phosphorylated.

Reagents (antibodies and AQUA peptides) provided by the invention may conveniently be grouped by the type of ATM and/or ATR kinase signaling protein in which a given phosphorylation site (for which reagents are provided) occurs. The protein types for each respective protein (in which a phosphorylation site has been discovered) are provided in Column C of Table 1/FIG. 2, and include: Adaptor/Scaffold proteins, Apoptosis proteins, Calcium-binding proteins, Cell Cycle Regulation proteins, DNA replication proteins, Channel proteins, Chaperone proteins, Contractile proteins, Cellular Metabolism enzymes, Cytoskeletal proteins, DNA repair proteins, DNA binding proteins, Endoplasmic reticulum protein, enzyme proteins, G protein and GTPase Activating proteins, Guanine Nucleotide Exchange Factors, Helicase proteins, Isomerase proteins, Ligase proteins, Methyltransferase proteins Lipid Kinases, Lipid Binding proteins, Lipid Phosphatases, Phosphatase proteins Mitochondrial proteins, Motor proteins, DNA Repair/Binding/Transcription proteins, Kinase Proteins, Phosphodiesterases, Proteases, Serine/Threonine Protein Kinase, Protein Phosphatases, RNA binding proteins, Transferase proteins Receptors, Secreted proteins, Translation/Transporter proteins, Ubiquitin Conjugating System proteins, and Vesicle proteins. Each of these distinct protein groups is considered a preferred subset of ATM and/or ATR signal transduction protein phosphorylation sites disclosed herein, and reagents for their detection/quantification may be considered a preferred subset of reagents provided by the invention.

Particularly preferred subsets of the phosphorylation sites (and their corresponding proteins) disclosed herein are those occurring on the following protein types/groups listed in Column C of Table 1/FIG. 2, DNA repair proteins, transcription proteins, kinase proteins, Phosphatases, G protein/GTPase Activating proteins/Guanine Nucleotide Exchange Factors, DNA replication proteins, DNA binding proteins, Disease associated proteins, Adaptor/Scaffold proteins, Cell cycle regulation proteins, Proteases, Methyltransferases and Ubiquitin conjugating proteins. Accordingly, among preferred subsets of reagents provided by the invention are isolated antibodies and AQUA peptides useful for the detection and/or quantification of the foregoing preferred protein/phosphorylation site subsets.

In one subset of preferred embodiments, there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds an DNA repair protein selected from Column A, Rows 90-100, of Table 1 only when phosphorylated at the threonine or serine listed in corresponding Column D, Rows 90-100, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 90-100, of Table 1 (SEQ ID NOs: 89-99), wherein said antibody does not bind said protein when not phosphorylated at said threonine or serine. (ii) An equivalent antibody to (i) above that only binds the DNA repair protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site). (iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of an DNA repair protein selected from Column A, Rows 90-100, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 90-100, of Table 1 (SEQ ID NOs: 89-99), which sequence comprises the phosphorylatable threonine or serine listed in corresponding Column D, Rows 90-100, of Table 1.

Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following DNA repair protein phosphorylation sites are particularly preferred: MRE11A (S648), NBS1 (S397), and NBS1 (S58) (see SEQ ID NOs: 91, 95 and 96).

In a second subset of preferred embodiments there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a Transcription protein selected from Column A, Rows 221-266, of Table 1 only when phosphorylated at the threonine or serine listed in corresponding Column D, Rows 221-266, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 221-266, of Table 1 (SEQ ID NOs: 220-265), wherein said antibody does not bind said protein when not phosphorylated at said threonine or serine. (ii) An equivalent antibody to (i) above that only binds the Transcription protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site). (iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Transcription protein selected from Column A, Rows 221-266, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 221-266, of Table 1 (SEQ ID NOs: 220-265), which sequence comprises the phosphorylatable threonine or serine listed in corresponding Column D, Rows 221-266, of Table 1.

Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following Transcription protein phosphorylation sites are particularly preferred: FOXJ2 (S161), MYT1L (S991), 53BP1 (S105), MYST2 (S50), NCOA2 (S716) and YAP1 (T973) (see SEQ ID NOs: 224, 230, 251, 257, 259 and 262).

In another subset of preferred embodiments there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a Protein Kinase selected from Column A, Rows 149 and 166-181, of Table 1 only when phosphorylated at the threonine or serine listed in corresponding Column D, Rows 149 and 166-181, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 149 and 166-181, of Table 1 (SEQ ID NOs: 148 and 165-180), wherein said antibody does not bind said protein when not phosphorylated at said threonine or serine. (ii) An equivalent antibody to (i) above that only binds the Protein Kinase when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site). (iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Protein Kinase selected from Column A, Rows 149 and 166-181, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 149 and 166-181, of Table 1 (SEQ ID NOs: 148 and 165-180), which sequence comprises the phosphorylatable threonine or serine listed in corresponding Column D, Rows 149 and 166-181, of Table 1.

Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following Protein Kinase phosphorylation sites are particularly preferred: NLK (T286) and WNK1 (S167) (see SEQ ID NOs: 172 and 180).

In still another subset of preferred embodiments there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a Phosphatase selected from Column A, Rows 157-161 and 182-192, of Table 1 only when phosphorylated at the threonine or serine listed in corresponding Column D, Rows 157-161 and 182-192, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 157-161 and 182-192, of Table 1 (SEQ ID NOs: 156-160 and 181-191), wherein said antibody does not bind said protein when not phosphorylated at said threonine or serine. (ii) An equivalent antibody to (i) above that only binds the Phosphatase when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site). (iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Phosphatase selected from Column A, Rows 157-161 and 182-192, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 157-161 and 182-192, of Table 1 (SEQ ID NOs: 156-160 and 181-191), which sequence comprises the phosphorylatable threonine or serine listed in corresponding Column D, Rows 157-161 and 182-192, of Table 1.

In still another subset of preferred embodiments there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a G protein/GTPase/Guanine nucleotide exchange factor selected from Column A, Rows 119-135, of Table 1 only when phosphorylated at the serine or threonine listed in corresponding Column D, Rows 119-135, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 119-135, of Table 1 (SEQ ID NOs: 118-134), wherein said antibody does not bind said protein when not phosphorylated at said serine or threonine. (ii) An equivalent antibody to (i) above that only binds the G protein/GTPase/Guanine nucleotide exchange factor when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site). (iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a G protein/GTPase/Guanine nucleotide exchange factor selected from Column A, Rows 119-135, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 119-135, of Table 1 (SEQ ID NOs: 118-134), which sequence comprises the phosphorylatable threonine or serine listed in corresponding Column D, Rows 119-135, of Table 1.

In still another subset of preferred embodiments there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a DNA replication protein selected from Column A, Rows 101-114, of Table 1 only when phosphorylated at the threonine or serine listed in corresponding Column D, Rows 101-114, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 101-114 of Table 1 (SEQ ID NOs: 100-113), wherein said antibody does not bind said protein when not phosphorylated at said threonine or serine. (ii) An equivalent antibody to (i) above that only binds the DNA replication protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site). (iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a DNA replication protein selected from Column A, Rows 101-114, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 101-114, of Table 1 (SEQ ID NOs: 100-113), which sequence comprises the phosphorylatable threonine or serine listed in corresponding Column D, Rows 101-114, of Table 1.

Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following DNA replication protein phosphorylation site is particularly preferred: SMC1 (S951) (see SEQ ID NO: 110).

In yet another subset of preferred embodiments, there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a DNA binding protein selected from Column A, Rows 70-89, of Table 1 only when phosphorylated at the threonine or serine listed in corresponding Column D, Rows 70-89, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 70-89, of Table 1 (SEQ ID NOs: 69-88), wherein said antibody does not bind said protein when not phosphorylated at said threonine or serine. (ii) An equivalent antibody to (i) above that only binds the DNA binding protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site). (iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a DNA binding protein that is a DNA binding protein selected from Column A, Rows 70-89, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 70-89, of Table 1 (SEQ ID NOs: 69-88), which sequence comprises the phosphorylatable threonine or serine listed in corresponding Column D, Rows 70-89, of Table 1.

In yet another subset of preferred embodiments, there is provided:

(i) An isolated phosphorylation site-specific antibody specifically binds a Disease associated protein selected from Column A, Rows 56-69, of Table 1 only when phosphorylated at the serine or threonine listed in corresponding Column D, Rows 56-69, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 56-69, of Table 1 (SEQ ID NOs: 55-68), wherein said antibody does not bind said protein when not phosphorylated at said serine or threonine. (ii) An equivalent antibody to (i) above that only binds the Disease associated protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site). (iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Disease associated protein selected from Column A, Rows 56-69, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 56-69, of Table 1 (SEQ ID NOs: 55-68), which sequence comprises the phosphorylatable serine or threonine listed in corresponding Column D, Rows 56-69, of Table 1.

Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following Disease associated protein phosphorylation site is particularly preferred: Bcl-9 (S352) (see SEQ ID NO: 57).

In yet another subset of preferred embodiments, there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds an Adaptor/Scaffold protein selected from Column A, Rows 2-22, of Table 1 only when phosphorylated at the serine or threonine listed in corresponding Column D, Rows 2-22, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 2-22, of Table 1 (SEQ ID NOs: 1-21), wherein said antibody does not bind said protein when not phosphorylated at said serine or threonine. (ii) An equivalent antibody to (i) above that only binds the Adaptor/Scaffold protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site). (iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Adaptor/Scaffold protein selected from Column A, Rows 2-22, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 2-22, of Table 1 (SEQ ID NOs: 1-21), which sequence comprises the phosphorylatable serine and threonine listed in corresponding Column D, Rows 2-22, of Table 1.

Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following Adaptor/Scaffold protein phosphorylation sites are particularly preferred: DOK-1 (S310) (see SEQ ID NO: 5).

In still another subset of preferred embodiments, there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a Cell cycle regulation protein selected from Column A, Rows 27-42, of Table 1 only when phosphorylated at the threonine or serine listed in corresponding Column D, Rows 27-42, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 27-42, of Table 1 (SEQ ID NOs: 26-41), wherein said antibody does not bind said protein when not phosphorylated at said threonine or serine. (ii) An equivalent antibody to (i) above that only binds the Cell cycle regulation protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site). (iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Cell cycle regulation protein selected from Column A, Rows 27-42, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 27-42, of Table 1 (SEQ ID NOs: 26-41), which sequence comprises the phosphorylatable threonine or serine listed in corresponding Column D, Rows 27-42, of Table 1.

Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following Cell cycle regulation protein phosphorylation sites are particularly preferred: KI-67 (S2925) and NuMA-1 (S395) (see SEQ ID NOs: 33 and 39).

In still another subset of preferred embodiments, there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a Protease selected from Column A, Rows 163-165, of Table 1 only when phosphorylated at the serine or threonine listed in corresponding Column D, Rows 163-165, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 163-165, of Table 1 (SEQ ID NOs: 162-164), wherein said antibody does not bind said protein when not phosphorylated at said serine or threonine. (ii) An equivalent antibody to (i) above that only binds the Protease when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site). (iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Protease selected from Column A, Rows 163-165, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 163-165, of Table 1 (SEQ ID NOs: 162-164), which sequence comprises the phosphorylatable serine or threonine listed in corresponding Column D, Rows 163-165, of Table 1.

In still another subset of preferred embodiments, there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a Methyltransferase selected from Column A, Rows 153-156, of Table 1 only when phosphorylated at the serine or threonine listed in corresponding Column D, Rows 153-156, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 153-156, of Table 1 (SEQ ID NOs: 152-155), wherein said antibody does not bind said protein when not phosphorylated at said serine or threonine. (ii) An equivalent antibody to (i) above that only binds the Methyltransferase when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site). (iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Methyltransferase selected from Column A, Rows 153-156, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 153-156, of Table 1 (SEQ ID NOs: 152-155), which sequence comprises the phosphorylatable serine or threonine listed in corresponding Column D, Rows 153-156, of Table 1.

In still another subset of preferred embodiments, there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a Ubiquitin conjugating protein selected from Column A, Rows 285-298, of Table 1 only when phosphorylated at the threonine or serine listed in corresponding Column D, Rows 285-298, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 285-298, of Table 1 (SEQ ID NOs: 284-297), wherein said antibody does not bind said protein when not phosphorylated at said threonine or serine. (ii) An equivalent antibody to (i) above that only binds the Ubiquitin conjugating protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site). (iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Ubiquitin conjugating protein selected from Column A, Rows 285-298, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 285-298, of Table 1 (SEQ ID NOs: 284-297), which sequence comprises the phosphorylatable threonine or serine listed in corresponding Column D, Rows 285-298, of Table 1.

Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following Ubiquitin conjugating protein phosphorylation sites are particularly preferred: UREB1 (T485) (see SEQ ID NO: 291).

The invention also provides, in part, an immortalized cell line producing an antibody of the invention, for example, a cell line producing an antibody within any of the foregoing preferred subsets of antibodies. In one preferred embodiment, the immortalized cell line is a rabbit hybridoma or a mouse hybridoma.

In certain other preferred embodiments, a heavy-isotope labeled peptide (AQUA peptide) of the invention (for example, an AQUA peptide within any of the foregoing preferred subsets of AQUA peptides) comprises a disclosed site sequence wherein the phosphorylatable threonine or serine is phosphorylated. In certain other preferred embodiments, a heavy-isotope labeled peptide of the invention comprises a disclosed site sequence wherein the phosphorylatable threonine or serine is not phosphorylated.

The foregoing subsets of preferred reagents of the invention should not be construed as limiting the scope of the invention, which, as noted above, includes reagents for the detection and/or quantification of disclosed phosphorylation sites on any of the other protein type/group subsets (each a preferred subset) listed in Column C of Table 1/FIG. 2.

Also provided by the invention are methods for detecting or quantifying a ATM and/or ATR kinase signaling protein that is threonine- or serine-phosphorylated, said method comprising the step of utilizing one or more of the above-described reagents of the invention to detect or quantify one or more ATM and/or ATR kinase signaling protein(s) selected from Column A of Table 1 only when phosphorylated at the threonine or serine listed in corresponding Column D of Table 1. In certain preferred embodiments of the methods of the invention, the reagents comprise a subset of preferred reagents as described above.

Also provided by the invention is a method for obtaining a phosphorylation profile of protein kinases that are phosphorylated in ATM and/or ATR kinase signaling pathways, said method comprising the step of utilizing one or more isolated antibody that specifically binds a protein kinase selected from Column A, Rows 149 and 166-181, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 149 and 166-181, of Table 1, comprised within the phosphorylation site sequence listed in corresponding Column E, Rows 138-165, of Table 1 (SEQ ID NOs: 148 and 165-180), to detect the phosphorylation of one or more of said protein kinases, thereby obtaining a phosphorylation profile for said kinases.

The identification of the disclosed novel ATM and/or ATR kinase signaling protein phosphorylation sites, and the standard production and use of the reagents provided by the invention are described in further detail below and in the Examples that follow.

All cited references are hereby incorporated herein, in their entirety, by reference. The Examples are provided to further illustrate the invention, and do not in any way limit its scope, except as provided in the claims appended hereto.

TABLE 1 Newly Discovered ATM and/or ATR Phosphorylation Sites. Stable Stable Protein Accession Phospho. Phosphorylation Site 1 Name No. Protein Type Residue Sequence SEQ ID NO 2 AKAP12 NP_005091.2 Adaptor/scaffold T1264 TEGtQEADQYADEK SEQ ID NO: 1 3 AKAP13 NP_006729.4 Adaptor/scaffold T1112 RENISHNtQDILIPNVLLSQEK SEQ ID NO: 2 4 AKAP13 NP_006729.4 Adaptor/scaffold S1123 RENISHNTQDILIPNVLLsQEK SEQ ID NO: 3 5 ATG16L1 NP_110430.5 Adaptor/scaffold S269 RLsQPAGGLLDSITNIFGR SEQ ID NO: 4 6 Dok1 NP_001372.1 Adaptor/scaffold S310 IAPCPsQDSLYSDPLDSTSAQAGEGVQR SEQ ID NO: 5 7 MACF1 NP_149033.2 Adaptor/scaffold S5511 SGGRKsLSQPTPPPMPILSQSEAKNPR SEQ ID NO: 6 8 MACF1 NP_149033.2 Adaptor/scaffold S5513 SGGRKSLsQPTPPPMPILSQSEAKNPR SEQ ID NO: 7 9 MACF1 NP_949033.2 Adaptor/scaffold S5506 sGGRKSLSQPTPPPMPILSQSEAKNPR SEQ ID NO: 8 10 MACF1 NP_149033.2 Adaptor/scaffold S5524 SGGRKSLSQPTPPPMPILsQSEAKNPR SEQ ID NO: 9 11 NDFIP2 NP_061953.1 Adaptor/scaffold S205 AAAMAAAAAETsQR SEQ ID NO: 10 12 rabenosyn NP_071735.2 Adaptor/scaffold S217 ESLSTHTSPsQSPNSVHGSRR SEQ ID NO: 11 5 13 RANBP3 NP_003615.1 Adaptor/scaffold S186 ALsQTVPSSGTNGVSLPADCTGAVPAASPD SEQ ID NO: 12 TAAWR 14 RANBP3 NP_003615.1 Adaptor/scaffold S211 ALSQTVPSSGTNGVSLPADCTGAVPAAsPD SEQ ID NO: 13 TAAWR 15 RANBP3 NP_003615.1 Adaptor/scaffold S125 TsSLTQFPPSQSEER SEQ ID NO: 14 16 RANBP3 NP_003615.1 Adaptor/scaffold S133 TSSLTQFPPsQSEER SEQ ID NO: 15 17 RANBP3 NP_003615.1 Adaptor/scaffold T124 tSSLTQFPPSQSEER SEQ ID NO: 16 18 RANBP3 NP_003615.1 Adaptor/scaffold S126 TSsLTQFPPSQSEER SEQ ID NO: 17 19 RANBP3 NP_003615.1 Adaptor/scaffold T128 TSSLtQFPPSQSEER SEQ ID NO: 18 20 RANBP3 NP_003615.1 Adaptor/scaffold S135 TSSLTQFPPSQsEER SEQ ID NO: 19 21 SAKS1 NP_056937.2 Adaptor/scaffold S202 YGGSVGSQPPPVAPEPGPVPSSPsQEPPT SEQ ID NO: 20 KR 22 VANGL1 NP_620409.1 Adaptor/scaffold S88 TEEVQDDNWGETTTAITGTSEHSIsQEDIAR SEQ ID NO: 21 23 acinus NP_055792.1 Apoptosis S132 HSTPHAAFQPNSQIGEEMSQNSFIK SEQ ID NO: 22 24 requiem NP_006259.1 Apoptosis S113 EGLIsQDGSSLEALLR SEQ ID NO: 23 25 UACA NP_060473.2 Apoptosis T181 PtICQLLIDRGADVNSRDK SEQ ID NO: 24 26 SDF4 NP_057260.2 Calcium-binding T193 LNEELKVDEEtQEVLENLKDR SEQ ID NO: 25 protein 27 CENPF NP_057427.3 Cell cycle regulation S1255 GDLETSNLQDMQsQEISGLKDCEIDAEEK SEQ ID NO: 26 28 CLASP1 NP_056097.1 Cell cycle regulation S1196 FSFRsQEDLNEPIKR SEQ ID NO: 27 29 CNAP1 NP_055680.2 Cell cycle regulation T577 LLNILGLIFKGPAAStQEKNPR SEQ ID NO: 28 30 cyclin C NP_005181.2 Cell cycle regulation S278 MPKPKPPPNSEGEQGPNGSQN5SYSQS SEQ ID NO: 29 31 cyclin C NP_005181.2 Cell cycle regulation S279 MPKPKPPPNSEGEQGPNGSQNSsYSQS SEQ ID NO: 30 32 cyclin C NP_005181.2 Cell cycle regulation S275 MPKPKPPPNSEGEQGPNGsQNSSYSQS SEQ ID NO: 31 33 cyclin C NP_005181.2 Cell cycle regulation S281 MPKPKPPPNSEGEQGPNGSQNSSYsQS SEQ ID NO: 32 34 KI-67 NP_002408.3 Cell cycle regulation S2925 AQPLEDLASFOELsQrPGHTEELANGAADS SEQ ID NO: 33 FTSAPK 35 MDC1 NP_055456.1 Cell cycle regulation T659 ENLTDLWDTDTLGEStQPQR SEQ ID NO: 34 36 MOC1 NP_055456.1 Cell cycle regulation S1086 QDGsQEAPEAPLSSELEPFHPKPK SEQ ID NO: 35 37 MDC1 NP_055456.1 Cell cycle regulation S513 sQASTTVDINTQVEK SEQ ID NO: 36 38 NIPA NP_057562.3 Cell cycle regulation S472 QSsQPAETDSMSLSEK SEQ ID NO: 37 39 NuMA-1 NP_006176.2 Cell cycle regulation T1744 LPRtQPDGTSVPGEPASPISQR SEQ ID NO: 38 40 NuMA-1 NP_006176.2 Cell cycle regulation S395 LSQLEEHLsQLQDNPPQEK SEQ ID NO: 39 41 TPX2 NP_036244.2 Cell cycle regulation S310 GCTIVKPFNLsQGK SEQ ID NO: 40 42 VCP NP_009057.1 Cell cycle regulation S754 FPSGNQGGAGPsQGSGGGTGGSVYTEDN SEQ ID NO: 41 DDDLYG 43 CLIC1 NP_001279.2 Channel, chloride S163 VLDNYLTSPLPEEVDETSAEDEGVsQR SEQ ID NO: 42 44 SCN2A NP_066287.2 Channel, sodium S629 HSNVSQAsRASR SEQ ID NO: 43 45 SCN2A NP_066287.2 Channel, sodium S632 HSNVSQASRAsR SEQ ID NO: 44 46 SCN2A NP_066287.2 Channel, sodium S626 HSNVsQASRASR SEQ ID NO: 45 47 TBCB NP_001272.2 Chaperone; S110 VEKYTIsQEAYDQR SEQ ID NO:46 Cytoskeletal protein 48 ELMO2 NP_573403.1 Cytoskeletal protein S517 QSERMSQDDFQSPPIVELR SEQ ID NO: 47 49 ezrin NP_003370.2 Cytoskeletal protein S539 QLLTLSSELsQAR SEQ ID NO: 48 50 lamin NP_005563.1 Cytoskeletal protein T394 LRLSPSPtSQR SEQ ID NO: 49 A/C 51 lamin NP_005563.1 Cytoskeletal protein S395 LRLSPSPTsQR SEQ ID NO: 50 A/C 52 NEXN NP_653174.2 Cytoskeletal protein T193 NMWDDDSPEMYKtISQEFLTPGK SEQ ID NO: 51 53 NEXN NP_653174.2 Cytoskeletal protein S195 TIsQEFLTPGK SEQ ID NO: 52 54 TMSB10 NP_066926.1 Cytoskeletal protein T23 TEtQEKNTLPTKETIEQEKR SEQ ID NO: 53 55 tubulin, NP_005991 .1 Cytoskeletal protein: S232 LIsQIVSSITASLR SEQ ID NO: 54 alpha-1 Motor protein 56 ataxin-3 NP_004984.2 Disease associated S265 NIsQDMTQTSGTNLTSEELR SEQ ID NO: 55 57 ataxin-3 NP_0049842 Disease associated T269 NISQDMtQTSGTNLTSEELR SEQ ID NO: 56 58 BcI-9 NP_004317.2 Disease associated S352 APPPPPVSSGEPPTLGENPDGLsQEQLEHR SEQ ID NO: 57 59 BCL9L NP_872363.1 Disease associated S942 SPTLSQVHsPLVTSPSANLK SEQ ID NO: 58 60 BCL9L NP_872363.1 Disease associated S938 SPTLsQVHSPLVTSPSANLK SEQ ID NO: 59 61 BCL9L NP_872363.1 Disease associated T946 SPTLSQVHSPLVtSPSANLK SEQ ID NO: 60 62 BCL9L NP_872363.1 Disease associated S947 SPTLSQVHSPLVTsPSANLK SEQ ID NO: 61 63 MAGE- NP_055414.2 Disease associated S162 AQETEAAPSQAPADEPEPESAAAQsQENQ SEQ ID NO: 62 D2 DTRPK 64 NBEAL1 XP_00113443 Disease associated S1299 RLsQISAGETEYNTQDSK SEQ ID NO: 63 2.1 65 PAGE1 NP_003776.2 Disease associated S144 GDGPDVQELGLPNPEEVKTPEEDEGQsQP SEQ ID NO: 64 66 PRCC NP_005984.3 Disease associated S267 QITQEEDDsDEEVAPENFFSLPEK SEQ ID NO: 65 67 PRCC NP_005954.3 Disease associated T261 QItQEEDDSDEEVAPENFFSLPEK SEQ ID NO: 66 68 SART2 NP_037484.1 Disease associated S797 IFAIsQQQQQQSK SEQ ID NO: 67 69 STEAP1 NP_036581.1 Disease associated S337 INKTEICsQL SEQ ID NO: 68 70 ARID1A NP_006006.3 DNA binding protein S604 FPPPQELsQDSFGSQASSAPSMTSSK SEQ ID NO: 69 71 ARID1B NP_059989.1 DNA binding protein S574 YQPQQDMsQEGYGTR SEQ ID NO: 70 72 CBX3 NP_009207.2 DNA binding protein S79 GFTDADNTWEPEENLDCPELIEAFLNsQK SEQ ID NO: 71 73 NUCB1 NP_006175.2 DNA binding protein S369 AQRLsQETEALGR SEQ ID NO: 72 74 RPA1 NP_002936.1 DNA binding protein T180 AAGPSLSHTSGGtQSK SEQ ID NO: 73 75 UKp68 NP_079100.2 DNA binding protein S450 LQIDPVMAETLQMsQDYYDMESMVHADTR SEQ ID NO: 74 76 UKp68 NP_079100.2 DNA binding protein S390 TRTsQEELLAEWQGQSR SEQ ID NO: 75 77 WDHD1 NP_009017.1 DNA binding protein T826 AAELTAtQVEEEEEEEDFRK SEQ ID NO: 76 78 ZAP NP_064504.2 DNA binding protein S327 ATDLGGTSQAGTsQR SEQ ID NO: 77 79 ZAP NP_064504.2 DNA binding protein S335 FLENGsQEDLLHGNPGSTYLASNSTSAPNWK SEQ ID NO: 78 80 ZMYM4 NP_005086.2 DNA binding protein S122 RVTQHEsDNENEIQIQNK SEQ ID NO: 79 81 ZMYM4 NP_005086.2 DNA binding protein T118 RVtQHESDNENEIQIQNK SEQ ID NO: 80 82 ZNF262 NP_005086.2 DNA binding protein T1070 KTLSQGESQtSEHELFLDTK SEQ ID NO: 81 83 ZNF262 NP_005086.2 DNA binding protein S1064 KTLsQGESQTSEHELFLDTK SEQ ID NO: 82 84 ZNF262 NP_005086.2 DNA binding protein S1068 KTLSQGEsQTSEHELFLDTK SEQ ID NO: 83 85 ZNF262 NP_005086.2 DNA binding protein S1071 KTLSQGESQTSEHELFLDTK SEQ ID NO: 84 86 ZNF262 NP_005086.2 DNA binding protein S1249 SDPLGsTQDHALSQESSEPGCR SEQ ID NO: 85 87 ZNF262 NP_005086.2 DNA binding protein T1250 SDPLGStQDHALSQESSEPGCR SEQ ID NO: 86 88 ZNF262 NP_005086.2 DNA binding protein S1256 SDPLGSTQDHALsQESSEPGCR SEQ ID NO: 87 89 Nucleolin NP_005372.2 DNA binding protein: T405 NLPYKVtQDELKEVFEDAAEIR SEQ ID NO: 88 Helicase; RNA binding protein 90 FANCA NP_000126.2 DNA repair S1449 QQAAPDADLsQEPHLF SEQ ID NO: 89 91 FANOD2 NP_149075.2 DNA repair T596 SESPSLtQER SEQ ID NO: 90 92 MRE11A NP_005581.2 DNA repair S648 IMsQSQVSK SEQ ID NO.91 93 MRE11A NP_005581.2 DNA repair S650 IMSQsQVSK SEQ ID NO: 92 94 NBS1 NP_002476.2 DNA repair S615 MDIETNDTFSDEAVPESSKIsQENEIGK SEQ ID NO: 93 95 NBS1 NP_002476.2 DNA repair S397 MLsQDAPTVK SEQ ID NO: 94 96 NBS1 NP_002476.2 DNA repair S58 NHAVLTANFSVTNLsQTDEIPVLTLK SEQ ID NO: 95 97 PMS2 NP_000526.1 DNA repair T597 LVNtQDMSASQVDVAVK SEQ ID NO: 96 98 RAD23A NP_005044.1 DNA repair S357 NENLAANFLLsQNFDDE SEQ ID NO: 97 99 Rif1 NP_060621.3 DNA repair T1518 KADPENIKSEGDGtQDIVDKSSEK SEQ ID NO: 98 100 TDP1 NP_060789.2 DNA repair S563 FFAGsQEPMATFPVPYDLPPELYGSK SEQ ID NO: 99 101 BAZ1A NP_038476.2 DNA replication S286 IHIsQEDNVANK SEQ ID NO: 100 102 CAF-1B NP_005432.1 DNA replication S409 GsSPGPRPVEGTPASRTQDPSSPGTTPPQAR SEQ ID NO: 101 103 CAF-1B NP_005432.1 DNA replication S410 GSsPGPRPVEGTPASRTQDPSSPGTTPPQAR SEQ ID NO: 102 104 CAF-1B NP_005432.1 DNA replication S428 GSSPGPRPVEGTPASRTQDPsSPGTTPPQAR SEQ ID NO: 103 105 CAF-1B NP_005432.1 DNA replication T424 GSSPGPRPVEGTPASRtQDPSSPGTTPPQAR SEQ ID NO: 104 106 PSF2 NP_057179.1 DNA replication T180 LRTNLQPLEStQSQDF SEQ ID NO: 105 107 PSF2 NP_057179.1 DNA replication S179 TNLQPLEsTQSQDF SEQ ID NO: 106 108 PSF2 NP_057179.1 DNA replication S182 TNLQPLESTQsQDF SEQ ID NO: 107 109 RFC1 NP_002904.3 DNA replication T193 RKELSQNtDESGLNDEAIAK SEQ ID NO: 108 110 RFC1 NP_002904.3 DNA replication S196 RKELSQNTDEsGLNDEAIAK SEQ ID NO: 109 111 Smc1 NP_006297.2 DNA replication S951 GTMDDIsQEEGSSQGEDSVSGSQR SEQ ID NO: 110 112 TERF2IP NP_061848.2 DNA replication S206 YLLGDAPVSPSsQK SEQ ID NO: 111 113 TOPBP1 NP_008958.1 DNA replication 8405 DFAPSEKHEQADEDLLsQYENGSSTWEAK SEQ ID NO: 112 114 TOPBP1 NP_008958.1 DNA replication T975 GVLtQTLEMR SEQ ID NO: 113 115 TOR1AI NP_659471.1 Endoplasmic S150 EASDGTGAsQEPPTTDSQEAQSPGHSSAG SEQ ID NO: 114 P2 reticulum QEGEDTLR 116 TOR1AI NP_659471.1 Endoplasmic S158 EASDGTGASQEPPTTDsQEAQSPGHSSAG SEQ ID NO: 115 P2 reticulum QEGEDTLR 117 GAPDH NP_002037.2 Enzyme, cellular T184 VIHDNFGIVEGLMYTVHAITAtQK SEQ ID NO: 116 metabolism 118 deoxyhy NP_001921.1 Enzyme, misc. S78 KLEPLsQDEDQHADLrQSR SEQ ID NO: 117 pusine synthase 119 CSN1 NP_004118.3 G protein regulator, T479 SPPREGSQGELtPANSQSR SEQ ID NO: 118 misc. 120 centauri- NP_056045.2 GTPase activating S580 NDWISILLNALKSQSLTsQSQAVVTPEK SEQ ID NO: 119 delta 1 protein, ARF 121 centauri- NP_056045.2 GTPase activating S582 NDWISILLNALKSQSLTSQsQAVVTPEK SEQ ID NO: 120 delta 1 protein, ARF 122 SIPA1L1 NP_0563711 GTPase activating T1190 SPASIDRQNtQSDIGGSGK SEQ ID NO: 121 protein, misc. 123 ARHGA NP_277050.2 GTPase activating S610 FLSQESGVAQTLK SEQ ID NO: 122 P18 protein, Rac/Rho 124 ARHGA NP_277050.2 GTPase activating S69 SISQDsLDELSMEDYWIELENIKK SEQ ID NO: 123 P18 protein, Rac/Rho 125 ARHGA NP_277050.2 GTPase activating S66 SIsQDSLDELSMEDYWIELENIKK SEQ ID NO: 124 P18 protein, Rac/Rho 126 ARHGA NP_038267.1 GTPase activating S569 AGPCSLsQGNLSPNWPR SEQ ID NO: 125 P6 protein, Rac/Rho 127 Cdc42E NP_008992.3 GTPase activating T34 RLtADMISHPLGDFR SEQ ID NO: 126 P1 protein, Rac/Rho 128 StARD13 NP_443083.1 GTPase activating S271 MHEFHsQENLWHIPK SEQ ID NO: 127 protein, Rac/Rho 129 ARHGE NP_004714.2 Guanine nucleotide S147 ILSQsTDSLNMR SEQ ID NO: 128 F2 exchange factor, Rac/Rho 130 ARHGE NP_004714.2 Guanine nucleotide S145 ILsQSTDSLNMR SEQ ID NO: 129 F2 exchange factor, Rac/Rho 131 ARHGE NP_004714.2 Guanine nucleotide T148 RILSQStDSLNMR SEQ ID NO: 130 F2 exchange factor, Rac/Rho 132 HAPIP NP_003938.1 Guanine nucleotide T1627 DGVEDIDSQGDGSSQPDtISIASR SEQ ID NO: 131 exchange factor, Rac/Rho 133 HAPIP NP_003938.1 Guanine nucleotide S1629 DGVEDIDSQGDGSSQPDTIsIASR SEQ ID NO: 132 exchange factor, Rac/Rho 134 HAPIP NP_003938.1 Guanine nucleotide S1632 DGVEDIDSQGDGSSQPDTISIAsR SEQ ID NO: 133 exchange factor, Rac/Rho 135 HAPIP NP_003938.1 Guanine nucleotide S1623 DGVEDIDSQGDGSsQPDTISIASR SEQ ID NO: 134 exchange factor, Rac/Rho 136 CHD-6 NP_115597.3 Helicase S1714 KVLsQEPSSFQESPSTNTESR SEQ ID NO: 135 137 DDX11 NP_004390.3 Helicase T465 QNPNtQSLSQTGTELK SEQ ID NO: 136 138 DDX11 NP_004390.3 Helicase S469 QNPNTQSLsQTGTELK SEQ ID NO: 137 139 DDX18 NP_006764.3 Helicase S74 QKPMNVGLSETQNGGMsQEAVGNIK SEQ ID NO: 138 140 DDX9 NP_001348.2 Helicase S321 LAQFEPsQR SEQ ID NO: 139 141 DFFA NP_998731.1 Hydrolase, esterase S257 QAPELSLSsQDLEVGGNQGH SEQ ID NO: 140 142 DFFA NP_004392.1 Hydrolase, esterase S107 WAYNNSDGGTAWIsQESFDVDETDSGAGLK SEQ ID NO: 141 143 AMPD2 NP_004028.3 Hydrolase, non- S168 QIsQDVKLEPDILLR SEQ ID NO: 142 esterase 144 RENT1 NP_002902.2 Hydrolase, non- S1116 AYQHGGVTGLsQY SEQ ID NO: 143 esterase 145 RENT1 NP_002902.2 Hydrolase, non- S1089 sQIOVALSQDSTYQGER SEQ ID NO: 144 esterase 146 RENT1 NP_002902.2 Hydrolase, non- S1096 SQIDVALsQDSTYQGER SEQ ID NO: 145 esterase 147 PPIL1 NP_006103.1 Isomerase T126 TLEENKEEEGSEPPKAEtQEGEPIAK SEQ ID NO: 146 148 PPIL1 NP_057143.1 Isomerase S149 VGMVETNsQDRPVDDVK SEQ ID NO: 147 149 deoxy- NP_000779.1 Kinase (non-protein) T64 WCNVQStQDEFEELTMSQK SEQ ID NO: 148 cytidine kinase 150 ACSS2 NP_061147.1 Ligase T264 AELGMGDStSQSPPIKR SEQ ID NO: 149 151 ACSS2 NP_061147.1 Ligase S267 AELGMGDSTSQsPPIKR SEQ ID NO: 150 152 ATP11C NP_375965.2 Lipid binding protein S445 GVTQEVDGLsQTDGTLTYFDKVDK SEQ ID NO: 151 153 BAT8 NP_006700.2 Methyltransferase S569 GDGVTPPAGTAAPAPPPLsQDVPGR SEQ ID NO: 152 154 COQ3 NP_059117.3 Methyltransferase S86 LYsTSQTTVDSGEVK SEQ ID NO: 153 155 COQ3 NP_059117.3 Methyltransferase T90 LYSTSQtTVDSGEvK SEQ ID NO: 154 156 COQ3 NP_059117.3 Methyltransferase S88 LYSTsQTTVDSGEVK SEQ ID NO: 155 157 Pnk1 NP_009185.2 Phosphatase T118 TPESQPDtPPGTPLVSQDEKR SEQ ID NO: 156 (non-protein) 158 Pnk1 NP_009185.2 Phosphatase S114 TPEsQPDTPPGTPLVSQDEKR SEQ ID NO: 157 (non-protein) 159 Pnk1 NP_009185.2 Phosphatase S126 TPESQPDTPPGTPLVsQDEKR SEQ ID NO: 158 (non-protein) 160 PTP1B NP_002818.1 PHOSPHATASE; S363 GSPLNAAPYGIEsMSQDTEVR SEQ ID NO: 159 Phosphatase; Protein phosphatase, tyrosine (non-receptor) 161 PTP1B NP_002818.1 PHOSPHATASE; S365 GSPLNAAPYGIESMsQDTEVR SEQ ID NO: 160 Phosphatase; Protein phosphatase, tyrosine (non-receptor) 162 PLCG1 NP_002651.2 Phospholipase S1264 YQQPFEDFRIsQEHLADHFDSR SEQ ID NO: 161 163 ST14 NP_068813.1 Protease (non- S203 WMLPPRARSLKSFVVTSWAFPTDsK SEQ ID NO: 162 proteasomal) 164 PSMC1 NP_002793.2 Protease S4 MGQsQSGGHGPGGGKK SEQ ID NO: 163 (proteasomal subunit) 165 PSMD4 NP_002801.1 Protease S266 MTIsQQEFGR SEQ ID NO: 164 (proteasomal subunit) 166 TIF1- NP_005753.1 Protein kinase S824 FSAVLVEPPPMSLPGAGLSsQELSGGpGDGP SEQ ID NO: 165 beta 167 BRDT NP_001717.2 Protein kinase, S196 TSISPLNWQGAsVNSSSQTMQVTK SEQ ID NO: 166 Ser/Thr (non- receptor) 168 BRDT NP_001717.2 Protein kinase, S199 TSISPLNWQGASVNsSSQTMQVTK SEQ ID NO: 167 Ser/Thr (non- receptor) 169 BRDT NP_001717.2 Protein kinase, S201 TSISPLNWQGASVNSSsQTAAQVTK SEQ ID NO: 168 Ser/Thr (non- receptor) 170 BRDT NP_001717.2 Protein kinase, S200 TSISPLNWQGASVNSsSQTAAQVTK SEQ ID NO: 169 Ser/Thr (non- receptor) 171 BRDT NP_001717.2 Protein kinase, T203 TSISPLNWQGASVNSSSQtAAQVTK SEQ ID NO: 170 Ser/Thr (non- receptor) 172 BRDT NP_001717.2 Protein kinase, T208 TSISPLNWQGASVNSSSQTMQVtK SEQ ID NO: 171 Ser/Thr (non- receptor) 173 NLK NP_057315.2 Protein kinase, T286 HMtQEVVTQYYR SEQ ID NO: 172 Ser/Thr (non- receptor) 174 RIPK2 NP_003812.1 Protein kinase, S176 MMSLsQSR SEQ ID NO: 173 Ser/Thr (non- receptor) 175 SMG1 NP_055907.3 Protein kinase, T3550 SNTGQKtQPDVMSQNAR SEQ ID NO: 174 Ser/Thr (non- receptor) 176 SMG1 NP_055907.3 Protein kinase, S3556 SNTGQKTQPDVMsQNAR SEQ ID NO: 175 Ser/Thr (non- receptor) 177 STK33 NP_112168.1 Protein kinase, T491 TPVtPSQGTATKYPAK SEQ ID NO: 176 Ser/Thr (non- receptor) 178 STK33 NP_112168.1 Protein kinase, T496 TPVTPSQGtATKYPAK SEQ ID NO: 177 Ser/Thr (non- receptor) 179 STK33 NP_112168.1 Protein kinase, S493 TPVTPsQGTATKYPAK SEQ ID NO: 178 Ser/Thr (non- receptor) 180 VRK1 NP_003375.1 Protein kinase, T378 EIEESKEPGVEDTEWSNtQTEEAIQTR SEQ ID NO: 179 Ser/Thr (non- receptor) 181 WNK1 NP_061852.1 Protein kinase, S167 PVsQPSLVGSK SEQ ID NO: 180 Ser/Thr (non- receptor) 182 PPP1R1 NP_060077.1 Protein T560 RStQGVTLTDLK SEQ ID NO. 181 2C phosphatase, regulatory subunit 183 PPP1R7 NP_002703.1 Protein S12 GAGQQQsQEMMEVDR SEQ ID NO. 182 phosphatase, regulatory subunit 184 PPM1G NP_002698.1 Protein S183 SGGGTGEEPGsQGLNGEAGPEDSTRETPS SEQ ID NO: 183 phosphatase, QENGPTAK Ser/Thr (non-receptor) 185 PPM1G NP_002698.1 Protein T199 SGGGTGEEPGSQGLNGEAGPEDSTREtPS SEQ ID NO: 184 phosphatase, Ser/Thr (non-receptor) 186 PPM1G NP_002698.1 Protein S201 SGGGTGEEPGSQGLNGEAGPEDSTRETPs SEQ ID NO: 185 phosphatase, QENGPTAK Ser/Thr (non-receptor) 187 EYA3 NP_001981.2 Protein S262 LSSGDPSTsPSLSQTTPSKDTDDQSR SEQ ID NO: 186 phosphatase, tyrosine (non-receptor) 188 EYA3 NP_001981.2 Protein S264 LSSGDPSTSPsLSQTTPSKDTDDQSRK SEQ ID NO: 187 phosphatase, tyrosine (non-receptor) 189 EYA3 NP_001981.2 Protein T268 LSSGDPSTSPSLSQtTPSKDTDDQSRK SEQ ID NO: 188 phosphatase, tyrosine (non-receptor) 190 EYA3 NP_001981.2 Protein S266 LSSGDPSTSPSLsQTTPSKDTDDQSRK SEQ ID NO: 189 phosphatase, tyrosine (non-receptor) 191 PTPN14 NP_005392.2 Protein S486 NLNIINTHAYNQPEDLVYsQPEMR SEQ ID NO: 190 phosphatase, tyrosine (non-receptor) 192 PTPN21 NP_008970.1 Protein S492 NLNIGSSYAYSRPAALVYsQPEIR SEQ ID NO: 191 phosphatase, tyrosine (non-receptor) 193 VEGFR-2 NP_0022441 Receptor tyrosine T1217 FHYONtAGISQYLQNSK SEQ ID NO: 192 kinase 194 OGFR NP_031372.2 Receptor, misc. S420 IALNLEGCALsQGSLR SEQ ID NO: 193 195 OGFR NP_031372.2 Receptor, misc. T325 KVEEEGSPGDPDHEAStQGR SEQ ID NO: 194 196 OGFR NP_031372.2 Receptor, misc. S315 KVEEEGsPGDPDHEASTQGR SEQ ID NO: 195 197 OGFR NP_031372.2 Receptor, misc. T426 tGTQEVGGQDPGEAVQPCR SEQ ID NO: 196 198 OGFR NP_031372.2 Receptor, misc. T428 TGtQEVGGQDPGEAVQPCR SEQ ID NO: 197 199 PDGFRL NP_006198.1 Receptor, misc. S254 AEAGGRsQISVK SEQ ID NO: 198 200 HEAB NP_006822.1 RNA binding protein S344 VGAPTIPDSCLPLGMsQEDNQLK SEQ ID NO: 199 201 POP4 NP_006618.1 RNA binding protein S10 SVIYHALsQK SEQ ID NO: 200 202 RALY NP_031393.2 RNA binding protein S279 TRDDGDEEGLLTHSEEELEHsQDTDADDG SEQ ID NO: 201 ALQ 203 RBM16 NP_055707.3 RNA binding protein T619 SSEPVKETVQTTQSPtPVEK SEQ ID NO: 202 204 RBM16 NP_055707.3 RNA binding protein T615 SSEPVKETVQTtQSPTPVEK SEQ ID NO: 203 205 RBM34 NP_055829.1 RNA binding protein S94 NEEEESTSQIERPLsQEPAK SEQ ID NO: 204 206 SFRS14 NP_055699.1 RNA binding protein T7 RItQETFDAVLQEK SEQ ID NO: 205 207 SFRS7 BAC03661.1 RNA binding protein S136 FLRLSQsP SEQ ID NO: 206 208 SFRS7 BA003661.1 RNA binding protein S134 FLRLsQSP SEQ ID NO: 207 209 SFRS8 NP_094583.2 RNA binding protein T642 KPQLtQEELEAK SEQ ID NO: 208 210 SRm300 NP_057417.3 RNA binding protein T383 HGGSPQPLAtTPLSQEPVNPPSEASPTR SEQ ID NO: 209 211 SRm300 NP.057417.3 RNA binding protein S395 HGGSPQPLATTPLSQEPVNPPsEASPTR SEQ ID NO: 210 212 SSA2 NP_094591.2 RNA binding protein S19 QIANsQDGYVWQVTDMNR SEQ ID NO: 211 213 UTP14A NP_006640.2 RNA binding protein S434 KRsELSQDAEPAGSQETK SEQ ID NO: 212 214 UTP14A NP_006640.2 RNA binding protein S453 KRSELSQDAEPAGSQETKDSGsQEVLSELR SEQ ID NO: 213 215 UTP14A NP_006640.2 RNA binding protein S14 LAESLLALsQQEELADLPK SEQ ID NO: 214 216 UTP14A NP_006640.2 RNA binding protein T448 RSELSQDAEPAGSQEtK SEQ ID NO: 215 217 UTP14A NP_006640.2 RNA binding protein S437 SELsQDAEPAGSQETK SEQ ID NO: 216 218 UTP14A NP_006640.2 RNA binding protein S445 SELSQDAEPAGsQETK SEQ ID NO: 217 219 TAF15 NP_003478.1 RNA binding protein; S94 QSSYSQQPYNNQGQQQNMESSGsQGGR SEQ ID NO: 218 Translation initiation complex 220 MFGE8 NP_005919.1 Secreted protein S42 NPCHNGGLCEEIsQEVR SEQ ID NO: 219 221 CUTL1 NP_853530.1 Transcription factor S734 QAPLsQSDITILTPK SEQ ID NO: 220 222 ELYS NP_056261.3 Transcription factor S1797 GLsQNQQIPQNSVTPR SEQ ID NO: 221 223 FBP3 NP_003925.1 Transcription factor S569 QQVAFYGQTLGQAQAHsQEQ SEQ ID NO: 222 224 FOXJ2 NP_060886.1 Transcription factor S164 RHPPDDDLSQDsPEQEASKSPR SEQ ID NO: 223 225 FOXJ2 NP_060886.1 Transcription factor S161 RHPPDDDLsQDSPEQEASKSPR SEQ ID NO: 224 226 FOXJ2 NP_060886.1 Transcription factor S172 RHPPDDDLSQDSPEQEASKsPR SEQ ID NO: 225 227 MBD1 NP_056669.1 Transcription factor T449 QEKADtQDEWTPGTAVLTSPVLVPGCPSK SEQ ID NO: 226 228 MCEF NP_055238.1 Transcription factor S836 TIsQSSSLK SEQ ID NO: 227 229 MYT1L NP_055840.2 Transcription factor S994 QKDGYLNGSQFsWKSVK SEQ ID NO: 228 230 MYT1L NP_055840.2 Transcription factor S997 QKDGYLNGSQFSWKSVK SEQ ID NO: 229 231 MYT1L NP_055840.2 Transcription factor S991 QKDGYLNGsQFSWKSVK SEQ ID NO: 230 232 RFX5 NP_000440.1 Transcription factor S605 EHVLQSSLsQEHKDPKATPP SEQ ID NO: 231 233 TCEAL3 NP116315.1 Transcription factor S65 REDEGEPGDEGQLEDEGsQEKQGR SEQ ID NO: 232 234 ZNF264 NP_003408.1 Transcription factor S80 KEDLsQDTCPGDKGKPK SEQ ID NO: 233 235 ZNF281 NP_036614.1 Transcription factor S395 GATSAEPGSSNHTNMGNLAVLsQGNTSSSR SEQ ID NO: 234 236 ZNF281 NP_036614.1 Transcription factor S807 NLESSTGFQIPsQELASQIDPQKDIEPR SEQ ID NO: 235 237 TAF1C NP_005670.2 Transcription S856 ATRSQQHTPVLsSSQPLRKKPR SEQ ID NO: 236 initiation complex 238 TAF1C NP_005670.2 Transcription S857 ATRSQQHTPVLSsSQPLRKKPR SEQ ID NO. 237 initiation complex 239 TAF1C NP_005670.2 Transcription S848 ATRsQQHTPVLSSSQPLRKKPR SEQ ID NO: 238 initiation complex 240 TAF1C NP_005670.2 Transcription S858 ATRSQQHTPVLSSsQPLRKKPR SEQ ID NO: 239 initiation complex 241 TFIIF NP_004119.1 Transcription S142 LQIEESSKPVRLsQQLDK SEQ ID NO: 240 initiation complex 242 SSRP1 NP_003137.1 Transcription T170 FYVPPtQEDGVDPVEAFAQNVLSK SEQ ID NO: 241 initiation complex; Transcription, coactivator/corepressor 243 53BP1 NP_005648.1 Transcription, T855 ADDPLRLDQELQQPQtQEK SEQ ID NO: 242 coactivator/corepressor 244 53BP1 NP_005648.1 Transcription, S580 FVPAENDSILMNPAQDGEVQLsQNDDKTK SEQ ID NO: 243 coactivator/corepressor 245 53BP1 NP_005648.1 Transcription, S566 FVPAENDsILMNPAQDGEVQLSQNDDKTK SEQ ID NO: 244 coactivator/corepressor 246 53BP1 NP_005648.1 Transcription, T543 IDEDGENtQIEDTEPMSPVLNSK SEQ ID NO: 245 coactivator/corepressor 247 53BP1 NP_005648.1 Transcription, T859 LDQELQQPQTQEKtSNSLTEDSK SEQ ID NO: 246 coactivator/corepressor 248 53BP1 NP_005648.1 Transcription, S860 LDQELQQPQTQEKTsNSLTEDSK SEQ ID NO: 247 coactivator/corepressor 249 53BP1 NP_005648.1 Transcription, S862 LDQELQQPQTQEKTSNsLTEDSK SEQ ID NO: 248 coactivator/corepressor 250 53BP1 NP_005648.1 Transcription, S1104 QSQQPMKPISPVKDPVSPAsQK SEQ ID NO: 249 coactivator/corepressor 251 53BP1 NP_005648.1 Transcription, T302 SPEPEVLStQEDLFDQSNK SEQ ID NO: 250 coactivator/corepressor 252 53BP1 NP_005648.1 Transcription, S105 VADPVDSSNLDTCGSIsQVIEQLPQPNR SEQ ID NO: 251 coactivator/corepressor 253 HBXAP NP_057662.3 Transcription, S524 DADSSISVLEIHsQK SEQ ID NO: 252 coactivator/corepressor 254 ILF2 NP_004506.2 Transcription, T388 AYEKPPEKKEGEEEEENTEEPPQGEEEES SEQ ID NO: 253 coactivator/corepressor MEtQE 255 MYST2 NP_008998.1 Transcription, S52 SSARLSQsSQDSSPVR SEQ ID NO: 254 coactivator/corepressor 256 MYST2 NP_008998.1 Transcription, S56 SSARLSQSSQDsSPVR SEQ ID NO: 255 coactivator/corepressor 257 MYST2 NP_008998.1 Transcription, S57 SSARLSQSSQDSsPVR SEQ ID NO: 256 coactivator/corepressor 258 MYST2 NP_008998.1 Transcription, S50 SSARLsQSSQDSSPVR SEQ ID NO: 257 coactivator/corepressor 259 MYST2 NP_008998.1 Transcription, S53 SSARLSQSsQDSSPVR SEQ ID NO: 258 coactivator/corepressor 260 NCOA2 NP_006531.1 Transcription, S716 LTAEATGKDLsQESSSTAPGSEVTIKQEPVS SEQ ID NO: 259 coactivator/corepressor PK 261 RBBP5 NP_005048.2 Transcription, S525 VQAELsQPLTAGGAISELL SEQ ID NO: 260 coactivator/corepressor 262 SLTM NP_00101386 Transcription, S955 EWHGPPsQGPSYHDTRR SEQ ID NO: 261 5.1 coactivator/corepressor 263 YAP1 NP_079031.2 Transcription, T973 SQLPTLEQDGGtQNPVSPGMSQELR SEQ ID NO: 262 coactivator/corepressor 264 YAP1 NP_006097.1 Transcription, S321 SQLPTLEQDGGTQNPVSSPGMsQELR SEQ ID NO: 263 coactivator/corepressor 265 ZNF318 NP_055160.2 Transcription, S214 YISQEEGPLsPFLGQLDEDYR SEQ ID NO: 264 coactivator/corepressor 266 ZNF318 NP_055160.2 Transcription, S207 YIsQEEGPLSPFLGQLDEDYR SEQ ID NO: 265 coactivator/corepressor 267 AASDH NP_056238.2 Transferase S258 HQDVPsQDDSKPTQR SEQ ID NO: 266 267 AASDH NP_056238.2 Transferase S258 HQDVPsQDDSKPTQR SEQ ID NO: 266 PPT 268 ATE1 NP_008972.2 Transferase S169 KEEPQELLQsQDFVGEK SEQ ID NO: 267 269 TGM7 NP_443187.1 Transterase T25 EHHtQEMGVKRLTVR SEQ ID NO: 268 270 UGP2 NP_006750.3 Transferase S13 AMsQDGASQFQEVIR SEQ ID NO: 269 271 eIF2B NP_003899.2 Translation initiation T31 KPFMLDEEGDtQTEETQPSETK SEQ ID NO: 270 complex 272 APT13A1 NP_065143.1 Transporter, active S817 DRLsQVLRDLEDESTPIVK SEQ ID NO: 271 273 NUP93 NP_055484.2 Transporter, active T159 ILHTLLASGEDALDFtQESEPSYISDVGPPG SEQ ID NO: 272 R 274 NUP93 NP_055464.2 Transporter, active S52 TLTRTsQETADVK SEQ ID NO: 273 275 SLC22A7 NP_696961.2 Transporter, active T409 LTQAGtLLGTALAFGTRLLVSSDMKSWSTVL SEQ ID NO: 274 AVMGK 276 SLC22A NP_696961.2 Transporter, active T405 LtQAGTLLGTALAFGTRLLVSSDMKSWSTVL SEQ ID NO: 275 AVMGK 277 SLC22A NP_696961.2 Transporter, active T419 LTQAGTLLGTALAFGtRLLVSSDMKSWSTVL SEQ ID NO: 276 AVMGK 278 SLC25A NP_001142.2 Transporter, active; T84 YFPtQALNFAFK Transporter, facilitator 279 NHE-1 NP_00308.2 Transporter, S787 SKETSSPGTDDVFTPAPSDSPsSQR SEQ ID NO: 278 facilitator 280 NHE-1 NP_003038.2 Transporter, S788 SKETSSPGTDDVFTPAPSDSPSsQR SEQ ID NO: 279 facilitator 281 NUP107 NP_0651M.1 Transporter, S37 VLLQAsQDENFGNTTPR SEQ ID NO: 280 facilitator 282 TPR NP_003283.2 Transporter, S2034 MDsQNSGEGNTGAAESSFSQEVSR SEQ ID NO: 281 facilitator 283 TPR NP_003283.2 Transporter, S2050 AADSQNSGEGNTGAAESSFsQEVSR SEQ ID NO: 282 facilitator 284 SASH1 NP_056093.3 Tumor suppressor S90 RVsQDLEVEKPDASPTSLQLR SEQ ID NO: 283 285 BRAP NP_006759.2 Ubiquitin conjugating T474 CtQLNTKVAKLTNELK SEQ ID NO: 284 system 286 BRAP NP_006759.2 Ubiquitin conjugating T484 CTQLNTKVAKLtNELK SEQ ID NO: 285 system 287 DCIN1 NP_0655691.2 Ubiquitin conjugating S31 TAVSCLsQNDWK SEQ ID NO: 286 system 288 HYD NP_056986.2 Ubiquitin conjugating S1549 RIsQSQPVR SEQ ID NO: 287 system 289 MUF1 NP_006360.3 Ubiquitin conjugating T327 RStQESLTAGGTDLKR SEQ ID NO: 288 system 290 NOT4 NP_037448.2 Ubiquitin conjugating S71 KPYPEDPAVYKPLsQEELQR SEQ ID NO: 289 system 291 UBLE1A NP_005491.1 Ubiquitin conjugating S185 VAKVsQGVEDGPDTKR SEQ ID NO: 290 system 292 UREB1 NP_113584.3 Ubiquitin conjugating T485 IQRPNTtQEGEEMETDMDGVQCIPQR SEQ ID NO: 291 system 293 UREB1 NP_113584.3 Ubiquitin conjugating S2372 sGEDESQEDVLMDEAPSNLSQASTLQANR SEQ ID NO: 292 system 294 UREB1 NP_113584.3 Ubiquitin conjugating S2394 SGEDESQEDVLMDEAPSNLSQAsTLQANR SEQ ID NO: 293 system 295 UREB1 NP_113584.3 Ubiquitin conjugating S2377 SGEDEsQEDVLMDEAPSNLSQASTLQANR SEQ ID NO: 294 system 296 UREB1 NP_113584.3 Ubiquitin conjugating S2391 SGEDESQEDVLMDEAPSNLsQASTLQANR SEQ ID NO: 295 system 297 USP29 NP_065954.1 Ubiquitin conjugating T17 tGMTKLKEALIETVQRQK SEQ ID NO: 296 system 298 U5P36 NP_079366.3 Ubiquitin conjugating S1053 MSAVsQDAIEDSR SEQ ID NO: 297 system 299 COG1 NP_061184.1 Vesicle protein T657 VKtQEIIPTQAK SEQ ID NO: 298 300 ICA1 NP_004959.2 Vesicle protein S100 FLRsQGFQDK SEQ ID NO: 299 301 SNX2S NP_114159.2 Vesicle protein S410 EEEKHAsQMISNK SEQ ID NO: 300

The short name for each protein in which a phosphorylation site has presently been identified is provided in Column A, and its SwissProt accession number (human) is provided Column B. The protein type/group into which each protein falls is provided in Column C. The identified threonine or serine residue at which phosphorylation occurs in a given protein is identified in Column D, and the amino acid sequence of the phosphorylation site encompassing the serine or threonine residue is provided in Column E (lower case t=the threonine, or lower case s=the serine (identified in Column D)) at which phosphorylation occurs. Table 1 above is identical to FIG. 2, except that the latter includes the disease and cell type(s) in which the particular phosphorylation site was identified (Columns F and G).

The identification of these 300 phosphorylation sites is described in more detail in Part A below and in Example 1.

DEFINITIONS

As used herein, the following terms have the meanings indicated:

“Antibody” or “antibodies” refers to all types of immunoglobulins, including IgG, IgM, IgA, IgD, and IgE, including Fab or antigen-recognition fragments thereof, including chimeric, polyclonal, and monoclonal antibodies. The term “does not bind” with respect to an antibody's binding to one phospho-form of a sequence means does not substantially react with as compared to the antibody's binding to the other phospho-form of the sequence for which the antibody is specific.

“ATM and/or ATR kinase signaling protein” means any protein (or poly-peptide derived therefrom) enumerated in Column A of Table 1/FIG. 2, which is disclosed herein as being phosphorylated in one or more of the disclosed cell line(s). ATM and/or ATR kinase signaling proteins may be serine/threonine kinases, or direct substrates of such kinases, or may be indirect substrates downstream of such kinases in signaling pathways. An ATM and/or ATR kinase signaling protein may also be phosphorylated in other cell lines harboring activated kinase activity.

“Heavy-isotope labeled peptide” (used interchangeably with AQUA peptide) means a peptide comprising at least one heavy-isotope label, which is suitable for absolute quantification or detection of a protein as described in WO/03016861, “Absolute Quantification of Proteins and Modified Forms Thereof by Multistage Mass Spectrometry” (Gygi et al.), further discussed below.

“Protein” is used interchangeably with polypeptide, and includes protein fragments and domains as well as whole protein.

“Phosphorylatable amino acid” means any amino acid that is capable of being modified by addition of a phosphate group, and includes both forms of such amino acid.

“Phosphorylatable peptide sequence” means a peptide sequence comprising a phosphorylatable amino acid.

“Phosphorylation site-specific antibody” means an antibody that specifically binds a phosphorylatable peptide sequence/epitope only when phosphorylated, or only when not phosphorylated, respectively. The term is used interchangeably with “phospho-specific” antibody.

A. Identification of Novel ATM and/or ATR Protein Phosphorylation Sites.

The nearly 300 novel ATM and/or ATR kinase signaling protein phosphorylation sites disclosed herein and listed in Table 1/FIG. 2 were discovered by employing the modified peptide isolation and characterization techniques described in “Immunoaffinity Isolation of Modified Peptides From Complex Mixtures,” U.S. Patent Publication No. 20030044848, Rush et al. (the teaching of which is hereby incorporated herein by reference, in its entirety) using cellular extracts from the following human glioblastoma-derived cell lines and patient samples: M059K, 293 T, M059J, M059K+J and human embryonic kidney cells. The isolation and identification of phosphopeptides from these cell lines, using an ATM/ATR substrate antibody and a phospho-Chk2(T26/S28)/VCP(S784) antibody, which recognize the phosphorylated motifs LS*Q and S*Q, respectively, is described in detail in Example 1 below. See Cell Signaling Technolgy Inc. 2006-2006 catalogue #'s 2851 and 2664, respectively. In addition to the nearly 300 previously unknown protein phosphorylation sites (threonine and serine) discovered, many known phosphorylation sites were also identified (not described herein). The immunoaffinity/mass spectrometric technique described in the '848 patent Publication (the “IAP” method)—and employed as described in detail in the Examples—is briefly summarized below.

The IAP method employed generally comprises the following steps: (a) a proteinaceous preparation (e.g. a digested cell extract) comprising phosphopeptides from two or more different proteins is obtained from an organism; (b) the preparation is contacted with at least one immobilized ATM/ATR substrate antibody or phospho-chk2(T26/S28)/VCP(S784) antibody; (c) at least one phosphopeptide specifically bound by the immobilized antibody in step (b) is isolated; and (d) the modified peptide isolated in step (c) is characterized by mass spectrometry (MS) and/or tandem mass spectrometry (MS-MS). Subsequently, (e) a search program (e.g. Sequest) may be utilized to substantially match the spectra obtained for the isolated, modified peptide during the characterization of step (d) with the spectra for a known peptide sequence. A quantification step employing, e.g. SILAC or AQUA, may also be employed to quantify isolated peptides in order to compare peptide levels in a sample to a baseline.

In the IAP method as employed herein, at least one immobilized ATM/ATR substrate antibody or phospho-chk2(T26/S28)/VCP(S784) antibody (commercially available from Cell Signaling Technology, Inc., Beverly, Mass., Cat #'s 2851 and 2664, respectively, recognizing the phosphorylated motifs LS*Q and S*Q) were used in the immunoaffinity step to isolate the widest possible number of phospho-threonine and phospho-serine containing peptides from the cell extracts.

-   -   Extracts from the following cell lines were employed: M059K, 293         T, M059J, M059K+J and human embryonic kidney cells. These cells         were treated with 50 mJ/m² UV and allowed to rest for two (2)         hours.

As described in more detail in the Examples, lysates were prepared from these cells line and digested with trypsin after treatment with DTT and iodoacetamide to alkylate cysteine residues. Before the immunoaffinity step, peptides were pre-fractionated by reversed-phase solid phase extraction using Sep-Pak C₁₈ columns to separate peptides from other cellular components. The solid phase extraction cartridges were eluted with varying steps of acetonitrile. Each lyophilized peptide fraction was redissolved in MOP IP buffer and treated with ATM/ATR substrate antibody or phospho-chk2(T26/S28)/VCP(S784) antibody immobilized on protein A-Sepharose or Protein A-Sepharose. Immunoaffinity-purified peptides were eluted with 0.15% TFA and a portion of this fraction was concentrated with Stage or Zip tips and analyzed by LC-MS/MS, using a ThermoFinnigan LCQ Deca XP Plus as well as LTQ ion trap mass spectrometer. Peptides were eluted from a 10 cm×75 μm reversed-phase column with a 45-min linear gradient of acetonitrile. MS/MS spectra were evaluated using the program Sequest with the NCBI human protein database.

This revealed a total of nearly 300 novel threonine or serine phosphorylation sites in signaling pathways affected by kinase activation or active in ATM/ATR cells. The identified phosphorylation sites and their parent proteins are enumerated in Table 1/FIG. 2. The threonine or serine (human sequence) at which phosphorylation occurs is provided in Column D, and the peptide sequence encompassing the phosphorylatable threonine or serine residue at the site is provided in Column E. FIG. 2 also shows the particular type of ATM/ATR associated disease (see Column G) and cell line(s) (see Column F) in which a particular phosphorylation site was discovered.

As a result of the discovery of these phosphorylation sites, phospho-specific antibodies and AQUA peptides for the detection of and quantification of these sites and their parent proteins may now be produced by standard methods, described below. These new reagents will prove highly useful in, e.g., studying the signaling pathways and events underlying the progression of ATM/ATR associated diseases and the identification of new biomarkers and targets for diagnosis and treatment of such diseases.

B. Antibodies and Cell Lines

Isolated phosphorylation site-specific antibodies that specifically bind a ATM and/or ATR kinase signaling protein disclosed in Column A of Table 1 only when phosphorylated (or only when not phosphorylated) at the corresponding amino acid and phosphorylation site listed in Columns D and E of Table 1/FIG. 2 may now be produced by standard antibody production methods, such as anti-peptide antibody methods, using the phosphorylation site sequence information provided in Column E of Table 1. For example, two previously unknown NBS DNA repair protein phosphorylation sites (serine 397 and 58) (see Rows 95 and 96 of Table 1/FIG. 2) are presently disclosed. Thus, antibodies that specifically bind either of these novel NBS DNA repair protein sites can now be produced, e.g. by immunizing an animal with a peptide antigen comprising all or part of the amino acid sequence encompassing the respective phosphorylated residue (e.g. a peptide antigen comprising the sequence set forth in Rows 95 and 96 respectively, Column E, of Table 1 (SEQ ID NOs: 94 and 95, respectively) (which encompasses the phosphorylated serine at positions 397 and 58 in NBS), to produce an antibody that only binds NBS kinase when phosphorylated at that site.

Polyclonal antibodies of the invention may be produced according to standard techniques by immunizing a suitable animal (e.g., rabbit, goat, etc.) with a peptide antigen corresponding to the ATM and/or ATR phosphorylation site of interest (i.e. a phosphorylation site enumerated in Column E of Table 1, which comprises the corresponding phosphorylatable amino acid listed in Column D of Table 1), collecting immune serum from the animal, and separating the polyclonal antibodies from the immune serum, in accordance with known procedures. For example, a peptide antigen corresponding to all or part of the novel Dok1 Adaptor/Scaffold phosphorylation site disclosed herein (SEQ ID NO: 5=IAPCPsQDSLYSDPLDSTSAQAGEGVQR, encompassing phosphorylated serine 310 (see Row 6 of Table 1)) may be used to produce antibodies that only bind Dok1 when phosphorylated at Ser310. Similarly, a peptide comprising all or part of any one of the phosphorylation site sequences provided in Column E of Table 1 may employed as an antigen to produce an antibody that only binds the corresponding protein listed in Column A of Table 1 when phosphorylated (or when not phosphorylated) at the corresponding residue listed in Column D. If an antibody that only binds the protein when phosphorylated at the disclosed site is desired, the peptide antigen includes the phosphorylated form of the amino acid. Conversely, if an antibody that only binds the protein when not phosphorylated at the disclosed site is desired, the peptide antigen includes the non-phosphorylated form of the amino acid.

Peptide antigens suitable for producing antibodies of the invention may be designed, constructed and employed in accordance with well-known techniques. See, e.g., ANTIBODIES: A LABORATORY MANUAL, Chapter 5, p. 75-76, Harlow & Lane Eds., Cold Spring Harbor Laboratory (1988); Czernik, Methods In Enzymology, 201: 264-283 (1991); Merrifield, J. Am. Chem. Soc. 85:21-49 (1962)).

It will be appreciated by those of skill in the art that longer or shorter phosphopeptide antigens may be employed. See Id. For example, a peptide antigen may comprise the full sequence disclosed in Column E of Table 1/FIG. 2, or it may comprise additional amino acids flanking such disclosed sequence, or may comprise of only a portion of the disclosed sequence immediately flanking the phosphorylatable amino acid (indicated in Column E by lowercase “t” or “s”). Typically, a desirable peptide antigen will comprise four or more amino acids flanking each side of the phosphorylatable amino acid and encompassing it. Polyclonal antibodies produced as described herein may be screened as further described below.

Monoclonal antibodies of the invention may be produced in a hybridoma cell line according to the well-known technique of Kohler and Milstein. See Nature 265:495-97 (1975); Kohler and Milstein, Eur. J. Immunol. 6: 511 (1976); see also, CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Ausubel et al. Eds. (1989). Monoclonal antibodies so produced are highly specific, and improve the selectivity and specificity of diagnostic assay methods provided by the invention. For example, a solution containing the appropriate antigen may be injected into a mouse or other species and, after a sufficient time (in keeping with conventional techniques), the animal is sacrificed and spleen cells obtained. The spleen cells are then immortalized by fusing them with myeloma cells, typically in the presence of polyethylene glycol, to produce hybridoma cells. Rabbit fusion hybridomas, for example, may be produced as described in U.S. Pat. No. 5,675,063, C. Knight, Issued Oct. 7, 1997. The hybridoma cells are then grown in a suitable selection media, such as hypoxanthine-aminopterin-thymidine (HAT), and the supernatant screened for monoclonal antibodies having the desired specificity, as described below. The secreted antibody may be recovered from tissue culture supernatant by conventional methods such as precipitation, ion exchange or affinity chromatography, or the like.

Monoclonal Fab fragments may also be produced in Escherichia coli by recombinant techniques known to those skilled in the art. See, e.g., W. Huse, Science 246:1275-81 (1989); Mullinax et al., Proc. Nat'l Acad. Sci. 87: 8095 (1990). If monoclonal antibodies of one isotype are preferred for a particular application, particular isotypes can be prepared directly, by selecting from the initial fusion, or prepared secondarily, from a parental hybridoma secreting a monoclonal antibody of different isotype by using the sib selection technique to isolate class-switch variants (Steplewski, et al., Proc. Nat'l. Acad. Sci., 82: 8653 (1985); Spira et al., J. Immunol. Methods, 74: 307 (1984)).

The preferred epitope of a phosphorylation-site specific antibody of the invention is a peptide fragment consisting essentially of about 8 to 17 amino acids including the phosphorylatable threonine or serine, wherein about 3 to 8 amino acids are positioned on each side of the phosphorylatable threonine (for example, the requiem serine 113 phosphorylation site sequence disclosed in Row 24, Column E of Table 1), and antibodies of the invention thus specifically bind a target ATM and/or ATR kinase signaling polypeptide comprising such epitopic sequence. Particularly preferred epitopes bound by the antibodies of the invention comprise all or part of a phosphorylatable site sequence listed in Column E of Table 1, including the phosphorylatable amino acid.

Included in the scope of the invention are equivalent non-antibody molecules, such as protein binding domains or nucleic acid aptamers, which bind, in a phospho-specific manner, to essentially the same phosphorylatable epitope to which the phospho-specific antibodies of the invention bind. See, e.g., Neuberger et al., Nature 312: 604 (1984). Such equivalent non-antibody reagents may be suitably employed in the methods of the invention further described below.

Antibodies provided by the invention may be any type of immunoglobulins, including IgG, IgM, IgA, IgD, and IgE, including Fab or antigen-recognition fragments thereof. The antibodies may be monoclonal or polyclonal and may be of any species of origin, including (for example) mouse, rat, rabbit, horse, or human, or may be chimeric antibodies. See, e.g., M. Walker et al., Molec. Immunol. 26: 403-11 (1989); Morrision et al., Proc. Nat'l. Acad. Sci. 81: 6851 (1984); Neuberger et al., Nature 312:604 (1984)). The antibodies may be recombinant monoclonal antibodies produced according to the methods disclosed in U.S. Pat. No. 4,474,893 (Reading) or U.S. Pat. No. 4,816,567 (Cabilly et al.) The antibodies may also be chemically constructed by specific antibodies made according to the method disclosed in U.S. Pat. No. 4,676,980 (Segel et al.)

The invention also provides immortalized cell lines that produce an antibody of the invention. For example, hybridoma clones, constructed as described above, that produce monoclonal antibodies to the ATM and/or ATR kinase signaling protein phosphorylation sties disclosed herein are also provided. Similarly, the invention includes recombinant cells producing an antibody of the invention, which cells may be constructed by well known techniques; for example the antigen combining site of the monoclonal antibody can be cloned by PCR and single-chain antibodies produced as phage-displayed recombinant antibodies or soluble antibodies in E. coli (see, e.g., ANTIBODY ENGINEERING PROTOCOLS, 1995, Humana Press, Sudhir Paul editor.)

Phosphorylation site-specific antibodies of the invention, whether polyclonal or monoclonal, may be screened for epitope and phospho-specificity according to standard techniques. See, e.g. Czemik et al., Methods in Enzymology, 201: 264-283 (1991). For example, the antibodies may be screened against the phospho and non-phospho peptide library by ELISA to ensure specificity for both the desired antigen (i.e. that epitope including a phosphorylation site sequence enumerated in Column E of Table 1) and for reactivity only with the phosphorylated (or non-phosphorylated) form of the antigen. Peptide competition assays may be carried out to confirm lack of reactivity with other phospho-epitopes on the given ATM and/or ATR kinase signaling protein. The antibodies may also be tested by Western blotting against cell preparations containing the signaling protein, e.g. cell lines over-expressing the target protein, to confirm reactivity with the desired phosphorylated epitope/target.

Specificity against the desired phosphorylated epitope may also be examined by constructing mutants lacking phosphorylatable residues at positions outside the desired epitope that are known to be phosphorylated, or by mutating the desired phospho-epitope and confirming lack of reactivity. Phosphorylation-site specific antibodies of the invention may exhibit some limited cross-reactivity to related epitopes in non-target proteins. This is not unexpected as most antibodies exhibit some degree of cross-reactivity, and anti-peptide antibodies will often cross-react with epitopes having high homology to the immunizing peptide. See, e.g., Czernik, supra. Cross-reactivity with non-target proteins is readily characterized by Western blotting alongside markers of known molecular weight. Amino acid sequences of cross-reacting proteins may be examined to identify sites highly homologous to the ATM and/or ATR kinase signaling protein epitope for which the antibody of the invention is specific.

In certain cases, polyclonal antisera may exhibit some undesirable general cross-reactivity to phosphothreonine or phosphoserine itself, which may be removed by further purification of antisera, e.g. over a phosphotyramine column. Antibodies of the invention specifically bind their target protein (i.e. a protein listed in Column A of Table 1) only when phosphorylated (or only when not phosphorylated, as the case may be) at the site disclosed in corresponding Columns D/E, and do not (substantially) bind to the other form (as compared to the form for which the antibody is specific).

Antibodies may be further characterized via immunohistochemical (IHC) staining using normal and diseased tissues to examine ATM and/or ATR phosphorylation and activation status in diseased tissue. IHC may be carried out according to well-known techniques. See, e.g., ANTIBODIES: A LABORATORY MANUAL, Chapter 10, Harlow & Lane Eds., Cold Spring Harbor Laboratory (1988). Briefly, paraffin-embedded tissue (e.g. tumor tissue) is prepared for immunohistochemical staining by deparaffinizing tissue sections with xylene followed by ethanol; hydrating in water then PBS; unmasking antigen by heating slide in sodium citrate buffer; incubating sections in hydrogen peroxide; blocking in blocking solution; incubating slide in primary antibody and secondary antibody; and finally detecting using ABC avidin/biotin method according to manufacturer's instructions.

Antibodies may be further characterized by flow cytometry carried out according to standard methods. See Chow et al., Cytometry (Communications in Clinical Cytometry) 46: 790-100 (2001). Briefly and by way of example, the following protocol for cytometric analysis may be employed: samples may be centrifuged on Ficoll gradients to remove erythrocytes, and cells may then be fixed with 2% paraformaldehyde for 10 minutes at 37° C. followed by permeabilization in 90% methanol for 30 minutes on ice. Cells may then be stained with the primary phosphorylation-site specific antibody of the invention (which detects a ATM and/or ATR signal transduction protein enumerated in Table 1), washed and labeled with a fluorescent-labeled secondary antibody. Additional fluorochrome-conjugated marker antibodies (e.g. CD45, CD34) may also be added at this time to aid in the subsequent identification of specific hematopoietic cell types. The cells would then be analyzed on a flow cytometer (e.g. a Beckman Coulter FC500) according to the specific protocols of the instrument used.

Antibodies of the invention may also be advantageously conjugated to fluorescent dyes (e.g. Alexa488, PE) for use in multi-parametric analyses along with other signal transduction (phospho-CrkL, phospho-Erk 1/2) and/or cell marker (CD34) antibodies.

Phosphorylation-site specific antibodies of the invention specifically bind to a human ATM and/or ATR signal transduction protein or polypeptide only when phosphorylated at a disclosed site, but are not limited only to binding the human species, per se. The invention includes antibodies that also bind conserved and highly homologous or identical phosphorylation sites in respective ATM and/or ATR proteins from other species (e.g. mouse, rat, monkey, yeast), in addition to binding the human phosphorylation site. Highly homologous or identical sites conserved in other species can readily be identified by standard sequence comparisons, such as using BLAST, with the human ATM and/or ATR signal transduction protein phosphorylation sites disclosed herein.

C. Heavy-Isotope Labeled Peptides (Aqua Peptides).

The novel ATM and/or ATR kinase signaling protein phosphorylation sites disclosed herein now enable the production of corresponding heavy-isotope labeled peptides for the absolute quantification of such signaling proteins (both phosphorylated and not phosphorylated at a disclosed site) in biological samples. The production and use of AQUA peptides for the absolute quantification of proteins (AQUA) in complex mixtures has been described. See WO/03016861, “Absolute Quantification of Proteins and Modified Forms Thereof by Multistage Mass Spectrometry,” Gygi et al. and also Gerber et al. Proc. Natl. Acad. Sci. U.S.A. 100: 6940-5 (2003) (the teachings of which are hereby incorporated herein by reference, in their entirety).

The AQUA methodology employs the introduction of a known quantity of at least one heavy-isotope labeled peptide standard (which has a unique signature detectable by LC-SRM chromatography) into a digested biological sample in order to determine, by comparison to the peptide standard, the absolute quantity of a peptide with the same sequence and protein modification in the biological sample. Briefly, the AQUA methodology has two stages: peptide internal standard selection and validation and method development; and implementation using validated peptide internal standards to detect and quantify a target protein in sample. The method is a powerful technique for detecting and quantifying a given peptide/protein within a complex biological mixture, such as a cell lysate, and may be employed, e.g., to quantify change in protein phosphorylation as a result of drug treatment, or to quantify differences in the level of a protein in different biological states.

Generally, to develop a suitable internal standard, a particular peptide (or modified peptide) within a target protein sequence is chosen based on its amino acid sequence and the particular protease to be used to digest. The peptide is then generated by solid-phase peptide synthesis such that one residue is replaced with that same residue containing stable isotopes (¹³C, ¹⁵N). The result is a peptide that is chemically identical to its native counterpart formed by proteolysis, but is easily distinguishable by MS via a 7-Da mass shift. A newly synthesized AQUA internal standard peptide is then evaluated by LC-MS/MS. This process provides qualitative information about peptide retention by reverse-phase chromatography, ionization efficiency, and fragmentation via collision-induced dissociation. Informative and abundant fragment ions for sets of native and internal standard peptides are chosen and then specifically monitored in rapid succession as a function of chromatographic retention to form a selected reaction monitoring (LC-SRM) method based on the unique profile of the peptide standard.

The second stage of the AQUA strategy is its implementation to measure the amount of a protein or modified protein from complex mixtures. Whole cell lysates are typically fractionated by SDS-PAGE gel electrophoresis, and regions of the gel consistent with protein migration are excised. This process is followed by in-gel proteolysis in the presence of the AQUA peptides and LC-SRM analysis. (See Gerber et al. supra.) AQUA peptides are spiked in to the complex peptide mixture obtained by digestion of the whole cell lysate with a proteolytic enzyme and subjected to immunoaffinity purification as described above. The retention time and fragmentation pattern of the native peptide formed by digestion (e.g. trypsinization) is identical to that of the AQUA internal standard peptide determined previously; thus, LC-MS/MS analysis using an SRM experiment results in the highly specific and sensitive measurement of both internal standard and analyte directly from extremely complex peptide mixtures. Because an absolute amount of the AQUA peptide is added (e.g. 250 fmol), the ratio of the areas under the curve can be used to determine the precise expression levels of a protein or phosphorylated form of a protein in the original cell lysate. In addition, the internal standard is present during in-gel digestion as native peptides are formed, such that peptide extraction efficiency from gel pieces, absolute losses during sample handling (including vacuum centrifugation), and variability during introduction into the LC-MS system do not affect the determined ratio of native and AQUA peptide abundances.

An AQUA peptide standard is developed for a known phosphorylation site sequence previously identified by the IAP-LC-MS/MS method within a target protein. One AQUA peptide incorporating the phosphorylated form of the particular residue within the site may be developed, and a second AQUA peptide incorporating the non-phosphorylated form of the residue developed. In this way, the two standards may be used to detect and quantify both the phosphorylated and non-phosphorylated forms of the site in a biological sample.

Peptide internal standards may also be generated by examining the primary amino acid sequence of a protein and determining the boundaries of peptides produced by protease cleavage. Alternatively, a protein may actually be digested with a protease and a particular peptide fragment produced can then sequenced. Suitable proteases include, but are not limited to, serine proteases (e.g. trypsin, hepsin), metallo proteases (e.g. PUMP1), chymotrypsin, cathepsin, pepsin, thermolysin, carboxypeptidases, etc.

A peptide sequence within a target protein is selected according to one or more criteria to optimize the use of the peptide as an internal standard. Preferably, the size of the peptide is selected to minimize the chances that the peptide sequence will be repeated elsewhere in other non-target proteins. Thus, a peptide is preferably at least about 6 amino acids. The size of the peptide is also optimized to maximize ionization frequency. Thus, peptides longer than about 20 amino acids are not preferred. The preferred ranged is about 7 to 15 amino acids. A peptide sequence is also selected that is not likely to be chemically reactive during mass spectrometry, thus sequences comprising cysteine, tryptophan, or methionine are avoided.

A peptide sequence that does not include a modified region of the target region may be selected so that the peptide internal standard can be used to determine the quantity of all forms of the protein. Alternatively, a peptide internal standard encompassing a modified amino acid may be desirable to detect and quantify only the modified form of the target protein. Peptide standards for both modified and unmodified regions can be used together, to determine the extent of a modification in a particular sample (i.e. to determine what fraction of the total amount of protein is represented by the modified form). For example, peptide standards for both the phosphorylated and unphosphorylated form of a protein known to be phosphorylated at a particular site can be used to quantify the amount of phosphorylated form in a sample.

The peptide is labeled using one or more labeled amino acids (i.e. the label is an actual part of the peptide) or less preferably, labels may be attached after synthesis according to standard methods. Preferably, the label is a mass-altering label selected based on the following considerations: The mass should be unique to shift fragment masses produced by MS analysis to regions of the spectrum with low background; the ion mass signature component is the portion of the labeling moiety that preferably exhibits a unique ion mass signature in MS analysis; the sum of the masses of the constituent atoms of the label is preferably uniquely different than the fragments of all the possible amino acids. As a result, the labeled amino acids and peptides are readily distinguished from unlabeled ones by the ion/mass pattern in the resulting mass spectrum. Preferably, the ion mass signature component imparts a mass to a protein fragment that does not match the residue mass for any of the 20 natural amino acids.

The label should be robust under the fragmentation conditions of MS and not undergo unfavorable fragmentation. Labeling chemistry should be efficient under a range of conditions, particularly denaturing conditions, and the labeled tag preferably remains soluble in the MS buffer system of choice. The label preferably does not suppress the ionization efficiency of the protein and is not chemically reactive. The label may contain a mixture of two or more isotopically distinct species to generate a unique mass spectrometric pattern at each labeled fragment position. Stable isotopes, such as ²H, ¹³C, ¹⁵N, ¹⁷O, ¹⁸O, or ³⁴S, are among preferred labels. Pairs of peptide internal standards that incorporate a different isotope label may also be prepared. Preferred amino acid residues into which a heavy isotope label may be incorporated include leucine, proline, valine, and phenylalanine.

Peptide internal standards are characterized according to their mass-to-charge (m/z) ratio, and preferably, also according to their retention time on a chromatographic column (e.g. an HPLC column). Internal standards that co-elute with unlabeled peptides of identical sequence are selected as optimal internal standards. The internal standard is then analyzed by fragmenting the peptide by any suitable means, for example by collision-induced dissociation (CID) using, e.g., argon or helium as a collision gas. The fragments are then analyzed, for example by multi-stage mass spectrometry (MS^(n)) to obtain a fragment ion spectrum, to obtain a peptide fragmentation signature. Preferably, peptide fragments have significant differences in m/z ratios to enable peaks corresponding to each fragment to be well separated, and a signature that is unique for the target peptide is obtained. If a suitable fragment signature is not obtained at the first stage, additional stages of MS are performed until a unique signature is obtained.

Fragment ions in the MS/MS and MS³ spectra are typically highly specific for the peptide of interest, and, in conjunction with LC methods, allow a highly selective means of detecting and quantifying a target peptide/protein in a complex protein mixture, such as a cell lysate, containing many thousands or tens of thousands of proteins. Any biological sample potentially containing a target protein/peptide of interest may be assayed. Crude or partially purified cell extracts are preferably employed. Generally, the sample has at least 0.01 mg of protein, typically a concentration of 0.1-10 mg/mL, and may be adjusted to a desired buffer concentration and pH.

A known amount of a labeled peptide internal standard, preferably about 10 femtomoles, corresponding to a target protein to be detected/quantified is then added to a biological sample, such as a cell lysate. The spiked sample is then digested with one or more protease(s) for a suitable time period to allow digestion. A separation is then performed (e.g. by HPLC, reverse-phase HPLC, capillary electrophoresis, ion exchange chromatography, etc.) to isolate the labeled internal standard and its corresponding target peptide from other peptides in the sample. Microcapillary LC is a preferred method.

Each isolated peptide is then examined by monitoring of a selected reaction in the MS. This involves using the prior knowledge gained by the characterization of the peptide internal standard and then requiring the MS to continuously monitor a specific ion in the MS/MS or MS^(n) spectrum for both the peptide of interest and the internal standard. After elution, the area under the curve (AUC) for both peptide standard and target peptide peaks are calculated. The ratio of the two areas provides the absolute quantification that can be normalized for the number of cells used in the analysis and the protein's molecular weight, to provide the precise number of copies of the protein per cell. Further details of the AQUA methodology are described in Gygi et al., and Gerber et al. supra.

In accordance with the present invention, AQUA internal peptide standards (heavy-isotope labeled peptides) may now be produced, as described above, for any of the nearly 300 novel ATM and/or ATR kinase signaling protein phosphorylation sites disclosed herein (see Table 1/FIG. 2). Peptide standards for a given phosphorylation site (e.g. the serine 395 in NuMA-1—see Row 40 of Table 1) may be produced for both the phosphorylated and non-phosphorylated forms of the site (e.g. see NuMA-1 site sequence in Column E, Row 41 of Table 1 (SEQ ID NO: 39) and such standards employed in the AQUA methodology to detect and quantify both forms of such phosphorylation site in a biological sample.

AQUA peptides of the invention may comprise all, or part of, a phosphorylation site peptide sequence disclosed herein (see Column E of Table 1/FIG. 2). In a preferred embodiment, an AQUA peptide of the invention comprises a phosphorylation site sequence disclosed herein in Table 1/FIG. 2. For example, an AQUA peptide of the invention for detection/quantification of MRE11A DNA repair protein when phosphorylated at serine S648 may comprise the sequence IMsQSQVSK (s=phosphoserine), which comprises phosphorylatable serine 648 (see Row 92, Column E; (SEQ ID NO: 91)). Heavy-isotope labeled equivalents of the peptides enumerated in Table 1/FIG. 2 (both in phosphorylated and unphosphorylated form) can be readily synthesized and their unique MS and LC-SRM signature determined, so that the peptides are validated as AQUA peptides and ready for use in quantification experiments.

The phosphorylation site peptide sequences disclosed herein (see Column E of Table 1/FIG. 2) are particularly well suited for development of corresponding AQUA peptides, since the IAP method by which they were identified (see Part A above and Example 1) inherently confirmed that such peptides are in fact produced by enzymatic digestion (trypsinization) and are in fact suitably fractionated/ionized in MS/MS. Thus, heavy-isotope labeled equivalents of these peptides (both in phosphorylated and unphosphorylated form) can be readily synthesized and their unique MS and LC-SRM signature determined, so that the peptides are validated as AQUA peptides and ready for use in quantification experiments.

Accordingly, the invention provides heavy-isotope labeled peptides (AQUA peptides) for the detection and/or quantification of any of the ATM and/or ATR phosphorylation sites disclosed in Table 1/FIG. 2 (see Column E) and/or their corresponding parent proteins/polypeptides (see Column A). A phosphopeptide sequence comprising any of the phosphorylation sequences listed in Table 1 may be considered a preferred AQUA peptide of the invention. For example, an AQUA peptide comprising the sequence PVsQPSLVGSK (SEQ ID NO: 180) (where s may be either phosphoserine or serine, and where V=labeled valine (e.g. ¹⁴C)) is provided for the quantification of phosphorylated (or non-phosphorylated) WNK1 kinase (Ser167) in a biological sample (see Row 181 of Table 1, serine 167 being the phosphorylatable residue within the site). However, it will be appreciated that a larger AQUA peptide comprising a disclosed phosphorylation site sequence (and additional residues downstream or upstream of it) may also be constructed. Similarly, a smaller AQUA peptide comprising less than all of the residues of a disclosed phosphorylation site sequence (but still comprising the phosphorylatable residue enumerated in Column D of Table 1/FIG. 2) may alternatively be constructed. Such larger or shorter AQUA peptides are within the scope of the present invention, and the selection and production of preferred AQUA peptides may be carried out as described above (see Gygi et al., Gerber et al. supra.).

Certain particularly preferred subsets of AQUA peptides provided by the invention are described above (corresponding to particular protein types/groups in Table 1, for example, Protein Kinases or Phosphatases). Example 4 is provided to further illustrate the construction and use, by standard methods described above, of exemplary AQUA peptides provided by the invention. For example, the above-described AQUA peptides corresponding to both the phosphorylated and non-phosphorylated forms of the disclosed WNK1 kinase serine, 167 phosphorylation site (see Row 181 of Table 1/FIG. 2) may be used to quantify the amount of phosphorylated WNK1 kinase (Ser167) in a biological sample, e.g. a tumor cell sample (or a sample before or after treatment with a test drug).

AQUA peptides of the invention may also be employed within a kit that comprises one or multiple AQUA peptide(s) provided herein (for the quantification of a ATM and/or ATR signal transduction protein disclosed in Table 1/FIG. 2), and, optionally, a second detecting reagent conjugated to a detectable group. For example, a kit may include AQUA peptides for both the phosphorylated and non-phosphorylated form of a phosphorylation site disclosed herein. The reagents may also include ancillary agents such as buffering agents and protein stabilizing agents, e.g., polysaccharides and the like. The kit may further include, where necessary, other members of the signal-producing system of which system the detectable group is a member (e.g., enzyme substrates), agents for reducing background interference in a test, control reagents, apparatus for conducting a test, and the like. The test kit may be packaged in any suitable manner, typically with all elements in a single container along with a sheet of printed instructions for carrying out the test.

AQUA peptides provided by the invention will be highly useful in the further study of signal transduction anomalies underlying cancer, including both solid and blood borne cancers, and in identifying diagnostic/bio-markers of these diseases, new potential drug targets, and/or in monitoring the effects of test compounds on ATM and/or ATR signal transduction proteins and pathways.

D. Immunoassay Formats

Antibodies provided by the invention may be advantageously employed in a variety of standard immunological assays (the use of AQUA peptides provided by the invention is described separately above). Assays may be homogeneous assays or heterogeneous assays. In a homogeneous assay the immunological reaction usually involves a phosphorylation-site specific antibody of the invention), a labeled analyte, and the sample of interest. The signal arising from the label is modified, directly or indirectly, upon the binding of the antibody to the labeled analyte. Both the immunological reaction and detection of the extent thereof are carried out in a homogeneous solution. Immunochemical labels that may be employed include free radicals, radioisotopes, fluorescent dyes, enzymes, bacteriophages, coenzymes, and so forth.

In a heterogeneous assay approach, the reagents are usually the specimen, a phosphorylation-site specific antibody of the invention, and suitable means for producing a detectable signal. Similar specimens as described above may be used. The antibody is generally immobilized on a support, such as a bead, plate or slide, and contacted with the specimen suspected of containing the antigen in a liquid phase. The support is then separated from the liquid phase and either the support phase or the liquid phase is examined for a detectable signal employing means for producing such signal. The signal is related to the presence of the analyte in the specimen. Means for producing a detectable signal include the use of radioactive labels, fluorescent labels, enzyme labels, and so forth. For example, if the antigen to be detected contains a second binding site, an antibody which binds to that site can be conjugated to a detectable group and added to the liquid phase reaction solution before the separation step. The presence of the detectable group on the solid support indicates the presence of the antigen in the test sample. Examples of suitable immunoassays are the radioimmunoassay, immunofluorescence methods, enzyme-linked immunoassays, and the like.

Immunoassay formats and variations thereof that may be useful for carrying out the methods disclosed herein are well known in the art. See generally E. Maggio, Enzyme-Immunoassay, (1980) (CRC Press, Inc., Boca Raton, Fla.); see also, e.g., U.S. Pat. No. 4,727,022 (Skold et al., “Methods for Modulating Ligand-Receptor Interactions and their Application”); U.S. Pat. No. 4,659,678 (Forrest et al., “Immunoassay of Antigens”); U.S. Pat. No. 4,376,110 (David et al., “Immunometric Assays Using Monoclonal Antibodies”). Conditions suitable for the formation of reagent-antibody complexes are well described. See id. Monoclonal antibodies of the invention may be used in a “two-site” or “sandwich” assay, with a single cell line serving as a source for both the labeled monoclonal antibody and the bound monoclonal antibody. Such assays are described in U.S. Pat. No. 4,376,110. The concentration of detectable reagent should be sufficient such that the binding of a target ATM and/or ATR signal transduction protein is detectable compared to background.

Phosphorylation site-specific antibodies disclosed herein may be conjugated to a solid support suitable for a diagnostic assay (e.g., beads, plates, slides or wells formed from materials such as latex or polystyrene) in accordance with known techniques, such as precipitation. Antibodies, or other target protein or target site-binding reagents, may likewise be conjugated to detectable groups such as radiolabels (e.g., ³⁵S, ¹²⁵I, ¹³¹I), enzyme labels (e.g., horseradish peroxidase, alkaline phosphatase), and fluorescent labels (e.g., fluorescein) in accordance with known techniques.

Antibodies of the invention may also be optimized for use in a flow cytometry (FC) assay to determine the activation/phosphorylation status of a target ATM and/or ATR signal transduction protein in patients before, during, and after treatment with a drug targeted at inhibiting phosphorylation at such a protein at the phosphorylation site disclosed herein. For example, bone marrow cells or peripheral blood cells from patients may be analyzed by flow cytometry for target ATM and/or ATR signal transduction protein phosphorylation, as well as for markers identifying various hematopoietic cell types. In this manner, activation status of the malignant cells may be specifically characterized. Flow cytometry may be carried out according to standard methods. See, e.g. Chow et al., Cytometry (Communications in Clinical Cytometry) 46: 72-78 (2001). Briefly and by way of example, the following protocol for cytometric analysis may be employed: fixation of the cells with 1% paraformaldehyde for 10 minutes at 37° C. followed by permeabilization in 90% methanol for 30 minutes on ice. Cells may then be stained with the primary antibody (a phospho-specific antibody of the invention), washed and labeled with a fluorescent-labeled secondary antibody. Alternatively, the cells may be stained with a fluorescent-labeled primary antibody. The cells would then be analyzed on a flow cytometer (e.g. a Beckman Coulter EPICS-XL) according to the specific protocols of the instrument used. Such an analysis would identify the presence of activated ATM and/or ATR signal transduction protein(s) in the malignant cells and reveal the drug response on the targeted protein.

Alternatively, antibodies of the invention may be employed in immunohistochemical (IHC) staining to detect differences in signal transduction or protein activity using normal and diseased tissues. IHC may be carried out according to well-known techniques. See, e.g., ANTIBODIES: A LABORATORY MANUAL, supra. Briefly, paraffin-embedded tissue (e.g. tumor tissue) is prepared for immunohistochemical staining by deparaffinizing tissue sections with xylene followed by ethanol; hydrating in water then PBS; unmasking antigen by heating slide in sodium citrate buffer; incubating sections in hydrogen peroxide; blocking in blocking solution; incubating slide in primary antibody and secondary antibody; and finally detecting using ABC avidin/biotin method according to manufacturer's instructions.

Antibodies of the invention may be also be optimized for use in other clinically-suitable applications, for example bead-based multiplex-type assays, such as IGEN, Luminex™ and/or Bioplex™ assay formats, or otherwise optimized for antibody arrays formats, such as reversed-phase array applications (see, e.g. Paweletz et al., Oncogene 20(16): 1981-89 (2001)). Accordingly, in another embodiment, the invention provides a method for the multiplex detection of ATM and/or ATR protein phosphorylation in a biological sample, the method comprising utilizing two or more antibodies or AQUA peptides of the invention to detect the presence of two or more phosphorylated ATM and/or ATR kinase signaling proteins enumerated in Column A of Table 1/FIG. 2. In one preferred embodiment, two to five antibodies or AQUA peptides of the invention are employed in the method. In another preferred embodiment, six to ten antibodies or AQUA peptides of the invention are employed, while in another preferred embodiment eleven to twenty such reagents are employed.

Antibodies and/or AQUA peptides of the invention may also be employed within a kit that comprises at least one phosphorylation site-specific antibody or AQUA peptide of the invention (which binds to or detects a ATM and/or ATR signal transduction protein disclosed in Table 1/FIG. 2), and, optionally, a second antibody conjugated to a detectable group. In some embodiments, the kit is suitable for multiplex assays and comprises two or more antibodies or AQUA peptides of the invention, and in some embodiments, comprises two to five, six to ten, or eleven to twenty reagents of the invention. The kit may also include ancillary agents such as buffering agents and protein stabilizing agents, e.g., polysaccharides and the like. The kit may further include, where necessary, other members of the signal-producing system of which system the detectable group is a member (e.g., enzyme substrates), agents for reducing background interference in a test, control reagents, apparatus for conducting a test, and the like. The test kit may be packaged in any suitable manner, typically with all elements in a single container along with a sheet of printed instructions for carrying out the test.

The following Examples are provided only to further illustrate the invention, and are not intended to limit its scope, except as provided in the claims appended hereto. The present invention encompasses modifications and variations of the methods taught herein which would be obvious to one of ordinary skill in the art.

Example 1 Isolation of Phosphoserine and/or Phosphothreonine-Containing Peptides from Extracts of Human Cancer Cell Lines and Identification of Novel Phosphorylation Sites

In order to discover previously unknown ATM and/or ATR signal transduction protein phosphorylation sites, IAP isolation techniques were employed to identify phosphothreonine- and/or phosphoserine-containing peptides in cell extracts from the following cell lines: M059K, 293 T, M059J, M059K+J and human embryonic kidney cells.

Tryptic phosphothreonine- and phosphoserine-containing peptides were purified and analyzed from extracts of each of the 3 cell lines mentioned above, as follows. Cells were cultured in DMEM medium (MO59K and J) or RPMI 1640 medium (293 cells) supplemented with 10% fetal bovine serum and penicillin/streptomycin. Cells were harvested by scraping plates. After complete aspiration of medium, cells were harvested in 10 mL lysis buffer per 2×10⁸ cells (20 mM HEPES pH 8.0, 9 M urea, 1 mM sodium vanadate, supplemented with 2.5 mM sodium pyro-phosphate, 1 mM β-glycerol-phosphate) and sonicated.

Sonicated cell lysates were cleared by centrifugation at 20,000×g, and proteins were reduced with DTT at a final concentration of 4.1 mM and alkylated with iodoacetamide at 8.3 mM. For digestion with trypsin, protein extracts were diluted in 20 mM HEPES pH 8.0 to a final concentration of 2 M urea and soluble TLCK-trypsin (Worthington) was added at 10-20 μg/mL. Digestion was performed for overnight days at room temperature.

Trifluoroacetic acid (TFA) was added to protein digests to a final concentration of 1%, precipitate was removed by centrifugation, and digests were loaded onto Sep-Pak C₁₈ columns (Waters) equilibrated with 0.1% TFA. A column volume of 0.7-1.0 ml was used per 2×10⁸ cells. Columns were washed with 15 volumes of 0.1% TFA, followed by 4 volumes of 5% acetonitrile (MeCN) in 0.1% TFA. Peptide fraction I was obtained by eluting columns with 2 volumes each of 8, 12, and 15% MeCN in 0.1% TFA and combining the eluates. Fractions II and III were a combination of eluates after eluting columns with 18, 22, 25% MeCN in 0.1% TFA and with 30, 35, 40% MeCN in 0.1% TFA, respectively. All peptide fractions were pooled and lyophilized.

Peptides from each fraction corresponding to 2×10⁸ cells were dissolved in 1 ml of IAP buffer (20 mM Tris/HCl or 50 mM MOPS pH 7.2, 10 mM sodium phosphate, 50 mM NaCl) and insoluble matter (mainly in peptide fractions III) was removed by centrifugation. IAP was performed on each peptide fraction separately. The ATM/ATR substrate antibody or phospho-chk2(T26/S28)/VCP(S784) antibody (commercially available from Cell Signaling Technology, Inc., Beverly, Mass., Cat #'s 2851 and 2664, respectively, recognizing the phosphorylated motifs LS*Q and S*Q) were coupled at 4 mg/ml beads to protein G or protein A agarose (Roche), respectively. Immobilized antibody (15 μl, 60 μg) was added as 1:1 slurry in IAP buffer to 1 ml of each peptide fraction, and the mixture was incubated overnight at 4° C. with gentle rotation. The immobilized antibody beads were washed three times with 1 ml IAP buffer and twice with 1 ml water, all at 4° C. Peptides were eluted from beads by incubation with 75 μl of 0.1% TFA at room temperature for 10 minutes.

Alternatively, one single peptide fraction was obtained from Sep-Pak C18 columns by elution with 2 volumes each of 10%, 15%, 20%, 25%, 30%, 35% and 40% acetonitirile in 0.1% TFA and combination of all eluates. IAP on this peptide fraction was performed as follows: After lyophilization, peptide was dissolved in 1.4 ml IAP buffer (MOPS pH 7.2, 10 mM sodium phosphate, 50 mM NaCl) and insoluble matter was removed by centrifugation. Immobilized antibody (40 μl, 160 μg) was added as 1:1 slurry in IAP buffer, and the mixture was incubated overnight at 4° C. with gentle shaking. The immobilized antibody beads were washed three times with 1 ml IAP buffer and twice with 1 ml water, all at 4° C. Peptides were eluted from beads by incubation with 55 μl of 0.15% TFA at room temperature for 10 min (eluate 1), followed by a second elution of the beads (eluate 2) with 45 μl of 0.15% TFA. Both eluates were combined.

Analysis by LC-MS/MS Mass Spectrometry.

40 μl or more of IAP eluate were purified by 0.2 μl StageTips or ZipTips. Peptides were eluted from the microcolumns with 1 μl of 40% MeCN, 0.1% TFA (fractions I and II) or 1 μl of 60% MeCN, 0.1% TFA (fraction III) into 7.6 μl of 0.4% acetic acid/0.005% heptafluorobutyric acid. This sample was loaded onto a 10 cm×75 μm PicoFrit capillary column (New Objective) packed with Magic C18 AQ reversed-phase resin (Michrom Bioresources) using a Famos autosampler with an inert sample injection valve (Dionex). The column was then developed with a 45-min linear gradient of acetonitrile delivered at 200 nl/min (Ultimate, Dionex), and tandem mass spectra were collected in a data-dependent manner with an LCQ Deca XP Plus ion trap mass spectrometer essentially as described by Gygi et al., supra.

Database Analysis & Assignments.

MS/MS spectra were evaluated using TurboSequest in the Sequest Browser package (v. 27, rev. 12) supplied as part of BioWorks 3.0 (ThermoFinnigan). Individual MS/MS spectra were extracted from the raw data file using the Sequest Browser program CreateDta, with the following settings: bottom MW, 700; top MW, 4,500; minimum number of ions, 20; minimum TIC, 4×10⁵; and precursor charge state, unspecified. Spectra were extracted from the beginning of the raw data file before sample injection to the end of the eluting gradient. The lonQuest and VuDta programs were not used to further select MS/MS spectra for Sequest analysis. MS/MS spectra were evaluated with the following TurboSequest parameters: peptide mass tolerance, 2.5; fragment ion tolerance, 0.0; maximum number of differential amino acids per modification, 4; mass type parent, average; mass type fragment, average; maximum number of internal cleavage sites, 10; neutral losses of water and ammonia from b and y ions were considered in the correlation analysis. Proteolytic enzyme was specified except for spectra collected from elastase digests.

Searches were performed against the NCBI human protein database (as released on Aug. 24, 2004 and containing 27,960 protein sequences). Cysteine carboxamidomethylation was specified as a static modification, and phosphorylation was allowed as a variable modification on serine and/or threonine. Furthermore, it should be noted that certain peptides were originally isolated in mouse and later normalized to human sequences as shown by Table1/FIG. 2.

In proteomics research, it is desirable to validate protein identifications based solely on the observation of a single peptide in one experimental result, in order to indicate that the protein is, in fact, present in a sample. This has led to the development of statistical methods for validating peptide assignments, which are not yet universally accepted, and guidelines for the publication of protein and peptide identification results (see Carr et al., Mol. Cell. Proteomics 3: 531-533 (2004)), which were followed in this Example. However, because the immunoaffinity strategy separates phosphorylated peptides from unphosphorylated peptides, observing just one phosphopeptide from a protein is a common result, since many phosphorylated proteins have only one threonine or serine phosphorylated site. For this reason, it is appropriate to use additional criteria to validate phosphopeptide assignments. Assignments are likely to be correct if any of these additional criteria are met: (i) the same sequence is assigned to co-eluting ions with different charge states, since the MS/MS spectrum changes markedly with charge state; (ii) the site is found in more than one peptide sequence context due to sequence overlaps from incomplete proteolysis or use of proteases other than trypsin; (iii) the site is found in more than one peptide sequence context due to homologous but not identical protein isoforms; (iv) the site is found in more than one peptide sequence context due to homologous but not identical proteins among species; and (v) sites validated by MS/MS analysis of synthetic phosphopeptides corresponding to assigned sequences, since the ion trap mass spectrometer produces highly reproducible MS/MS spectra. The last criterion is routinely employed to confirm novel site assignments of particular interest.

All spectra and all sequence assignments made by Sequest were imported into a relational database. The following Sequest scoring thresholds were used to select phosphopeptide assignments that are likely to be correct: RSp<6, XCorr≧2.2, and DeltaCN>0.099. Further, the assigned sequences could be accepted or rejected with respect to accuracy by using the following conservative, two-step process.

In the first step, a subset of high-scoring sequence assignments should be selected by filtering for XCorr values of at least 1.5 for a charge state of +1, 2.2 for +2, and 3.3 for +3, allowing a maximum RSp value of 10. Assignments in this subset should be rejected if any of the following criteria were satisfied: (i) the spectrum contains at least one major peak (at least 10% as intense as the most intense ion in the spectrum) that can not be mapped to the assigned sequence as an a, b, or y ion, as an ion arising from neutral-loss of water or ammonia from a b or y ion, or as a multiply protonated ion; (ii) the spectrum does not contain a series of b or y ions equivalent to at least six uninterrupted residues; or (iii) the sequence is not observed at least five times in all the studies conducted (except for overlapping sequences due to incomplete proteolysis or use of proteases other than trypsin).

In the second step, assignments with below-threshold scores should be accepted if the low-scoring spectrum shows a high degree of similarity to a high-scoring spectrum collected in another study, which simulates a true reference library-searching strategy.

Example 2 Production of Phospho-Specific Polyclonal Antibodies for the Detection of ATM and/or ATR Kinase Signaling Protein Phosphorylation

Polyclonal antibodies that specifically bind a ATM and/or ATR signal transduction protein only when phosphorylated at the respective phosphorylation site disclosed herein (see Table 1/FIG. 2) are produced according to standard methods by first constructing a synthetic peptide antigen comprising the phosphorylation site sequence and then immunizing an animal to raise antibodies against the antigen, as further described below. Production of exemplary polyclonal antibodies is provided below.

A. MYT1L (Serine 991).

A 17 amino acid phospho-peptide antigen, QKDGYLNGs*QFSWKSVK (where s*=phosphoserine) that corresponds to the sequence encompassing the serine 991 phosphorylation site in human MYT1L transcription factor (see Row 231 of Table 1; SEQ ID NO: 230), plus cysteine on the C-terminal for coupling, is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer. See ANTIBODIES: A LABORATORY MANUAL, supra.; Merrifield, supra. This peptide is then coupled to KLH and used to immunize animals to produce (and subsequently screen) phospho-specific MYT1L (ser 991) polyclonal antibodies as described in Immunization/Screening below.

B. MYST2 (Serine 50).

A 16 amino acid phospho-peptide antigen, SSARLs*QSSQDSSPVR (where s*=phosphoserine) that corresponds to the sequence encompassing the serine 50 phosphorylation site in human MYST2 transcription protein (see Row 258 of Table 1 (SEQ ID NO: 257)), plus cysteine on the C-terminal for coupling, is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer. See ANTIBODIES: A LABORATORY MANUAL, supra.; Merrifield, supra. This peptide is then coupled to KLH and used to immunize animals to produce (and subsequently screen) phospho-specific MYST2 (ser 50) polyclonal antibodies as described in Immunization/Screening below.

C. MRE11A (Serine 648).

A 9 amino acid phospho-peptide antigen, IMs*QSQVSK (where s*=phosphoserine) that corresponds to the sequence encompassing the serine 648 phosphorylation site in human MRE11A DNA repair protein (see Row 92 of Table 1 (SEQ ID NO: 91), plus cysteine on the C-terminal for coupling, is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer. See ANTIBODIES: A LABORATORY MANUAL, supra.; Merrifield, supra. This peptide is then coupled to KLH and used to immunize animals to produce (and subsequently screen) phospho-specific MRE11A (ser 648) antibodies as described in Immunization/Screening below.

Immunization/Screening.

A synthetic phospho-peptide antigen as described in A-C above is coupled to KLH, and rabbits are injected intradermally (ID) on the back with antigen in complete Freunds adjuvant (500 μg antigen per rabbit). The rabbits are boosted with same antigen in incomplete Freund adjuvant (250 μg antigen per rabbit) every three weeks. After the fifth boost, bleeds are collected. The sera are purified by Protein A-affinity chromatography by standard methods (see ANTIBODIES: A LABORATORY MANUAL, Cold Spring Harbor, supra.). The eluted immunoglobulins are further loaded onto a non-phosphorylated synthetic peptide antigen-resin Knotes column to pull out antibodies that bind the non-phosphorylated form of the phosphorylation site. The flow through fraction is collected and applied onto a phospho-synthetic peptide antigen-resin column to isolate antibodies that bind the phosphorylated form of the site. After washing the column extensively, the bound antibodies (i.e. antibodies that bind a phosphorylated peptide described in A-C above, but do not bind the non-phosphorylated form of the peptide) are eluted and kept in antibody storage buffer.

The isolated antibody is then tested for phospho-specificity using Western blot assay using an appropriate cell line that expresses (or overexpresses) target phospho-protein (i.e. phosphorylated MYTL1, MYST2 and MRE11A), for example, M059J, M059K M059K+J respectively. Cells are cultured in DMEM or RPMI supplemented with 10% FBS. Cell are collected, washed with PBS and directly lysed in cell lysis buffer. The protein concentration of cell lysates is then measured. The loading buffer is added into cell lysate and the mixture is boiled at 100° C. for 5 minutes. 20 μl (10 μg protein) of sample is then added onto 7.5% SDS-PAGE gel.

A standard Western blot may be performed according to the Immunoblotting Protocol set out in the CELL SIGNALING TECHNOLOGY, INC. 2003-04 Catalogue, p. 390. The isolated phospho-specific antibody is used at dilution 1:1000. Phosphorylation-site specificity of the antibody will be shown by binding of only the phosphorylated form of the target protein. Isolated phospho-specific polyclonal antibody does not (substantially) recognize the target protein when not phosphorylated at the appropriate phosphorylation site in the non-stimulated cells (e.g. MYTL1 is not bound when not phosphorylated at serine 74).

In order to confirm the specificity of the isolated antibody, different cell lysates containing various phosphorylated signal transduction proteins other than the target protein are prepared. The Western blot assay is performed again using these cell lysates. The phospho-specific polyclonal antibody isolated as described above is used (1:1000 dilution) to test reactivity with the different phosphorylated non-target proteins on Western blot membrane. The phospho-specific antibody does not significantly cross-react with other phosphorylated signal transduction proteins, although occasionally slight binding with a highly homologous phosphorylation-site on another protein may be observed. In such case the antibody may be further purified using affinity chromatography, or the specific immunoreactivity cloned by rabbit hybridoma technology.

Example 3 Production of Phospho-Specific Monoclonal Antibodies for the Detection of ATM and/or ATR Kinase Signaling Protein Phosphorylation

Monoclonal antibodies that specifically bind a ATM and/or ATR signal transduction protein only when phosphorylated at the respective phosphorylation site disclosed herein (see Table 1/FIG. 2) are produced according to standard methods by first constructing a synthetic peptide antigen comprising the phosphorylation site sequence and then immunizing an animal to raise antibodies against the antigen, and harvesting spleen cells from such animals to produce fusion hybridomas, as further described below. Production of exemplary monoclonal antibodies is provided below.

A. Requiem (Serine 113).

A 16 amino acid phospho-peptide antigen, EGLIs*QDGSSLEALLR (where s*=phosphoserine) that corresponds to the sequence encompassing the serine 113 phosphorylation site in human requiem apoptosis protein (see Row 24 of Table 1 (SEQ ID NO: 23)), plus cysteine on the C-terminal for coupling, is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer. See ANTIBODIES: A LABORATORY MANUAL, supra.; Merrifield, supra. This peptide is then coupled to KLH and used to immunize animals and harvest spleen cells for generation (and subsequent screening) of phospho-specific monoclonal requiem (ser 113) antibodies as described in Immunization/Fusion/Screening below.

B. NuMA-1 (Serine 395).

A 19 amino acid phospho-peptide antigen LSQLEEHLs*QLQDNPPQEK (where s*=phosphoserine) that corresponds to the sequence encompassing the serine 395 phosphorylation site in human NuMA-1 cell cycle regulation protein (see Row 40 of Table 1 (SEQ ID NO: 39)), plus cysteine on the C-terminal for coupling, is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer. See ANTIBODIES: A LABORATORY MANUAL, supra.; Merrifield, supra. This peptide is then coupled to KLH and used to immunize animals and harvest spleen cells for generation (and subsequent screening) of phospho-specific monoclonal NuMA-1 (ser395) antibodies as described in Immunization/Fusion/Screening below.

C. NLK (Threonine 286).

A 12 amino acid phospho-peptide antigen, HMt*QEVVTQYYR (where t*=phosphothreonine) that corresponds to the sequence encompassing the threonine 286 phosphorylation site in human NLK protein kinase (see Row 173 of Table 1 (SEQ ID NO: 172)), plus cysteine on the C-terminal for coupling, is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer. See ANTIBODIES: A LABORATORY MANUAL, supra.; Merrifield, supra. This peptide is then coupled to KLH and used to immunize animals and harvest spleen cells for generation (and subsequent screening) of phospho-specific monoclonal NLK (thr286) antibodies as described in Immunization/Fusion/Screening below.

Immunization/Fusion/Screening.

A synthetic phospho-peptide antigen as described in A-C above is coupled to KLH, and BALB/C mice are injected intradermally (ID) on the back with antigen in complete Freunds adjuvant (e.g. 50 μg antigen per mouse). The mice are boosted with same antigen in incomplete Freund adjuvant (e.g. 25 μg antigen per mouse) every three weeks. After the fifth boost, the animals are sacrificed and spleens are harvested.

Harvested spleen cells are fused to SP2/0 mouse myeloma fusion partner cells according to the standard protocol of Kohler and Milstein (1975). Colonies originating from the fusion are screened by ELISA for reactivity to the phospho-peptide and non-phospho-peptide forms of the antigen and by Western blot analysis (as described in Example 1 above). Colonies found to be positive by ELISA to the phospho-peptide while negative to the non-phospho-peptide are further characterized by Western blot analysis. Colonies found to be positive by Western blot analysis are subcloned by limited dilution. Mouse ascites are produced from a single clone obtained from subcloning, and tested for phospho-specificity (against the requiem, NuMA-1, or NLK phospho-peptide antigen, as the case may be) on ELISA. Clones identified as positive on Western blot analysis using cell culture supernatant as having phospho-specificity, as indicated by a strong band in the induced lane and a weak band in the uninduced lane of the blot, are isolated and subcloned as clones producing monoclonal antibodies with the desired specificity.

Ascites fluid from isolated clones may be further tested by Western blot analysis. The ascites fluid should produce similar results on Western blot analysis as observed previously with the cell culture supernatant, indicating phospho-specificity against the phosphorylated target (e.g. NLK phosphorylated at threonine 286).

Example 4 Production and Use of Aqua Peptides for the Quantification of ATM and/or ATR Kinase Signaling Protein Phosphorylation

Heavy-isotope labeled peptides (AQUA peptides (internal standards)) for the detection and quantification of a ATM and/or ATR signal transduction protein only when phosphorylated at the respective phosphorylation site disclosed herein (see Table 1/FIG. 2) are produced according to the standard AQUA methodology (see Gygi et al., Gerber et al., supra.) methods by first constructing a synthetic peptide standard corresponding to the phosphorylation site sequence and incorporating a heavy-isotope label. Subsequently, the MS^(n) and LC-SRM signature of the peptide standard is validated, and the AQUA peptide is used to quantify native peptide in a biological sample, such as a digested cell extract. Production and use of exemplary AQUA peptides is provided below.

A. WNK1 (Serine 167).

An AQUA peptide comprising the sequence, PVs*QPSLVGSK (s*=phosphoserine; sequence incorporating ¹⁴C/¹⁵N-labeled leucine (indicated by bold L), which corresponds to the serine 167 phosphorylation site in human WNK1 kinase (see Row 181 in Table 1 (SEQ ID NO: 180)), is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer (see Merrifield, supra.) as further described below in Synthesis & MS/MS Signature. The WNK1 (ser167) AQUA peptide is then spiked into a biological sample to quantify the amount of phosphorylated WNK1 (ser167) in the sample, as further described below in Analysis & Quantification.

B. 53BP1 (Serine 105).

An AQUA peptide comprising the sequence VADPVDSSNLDTCGSIs*QVIEQLPQPNR (s*=phosphoserine; sequence incorporating ¹⁴C/¹⁵N-labeled leucine (indicated by bold L), which corresponds to the serine 105 phosphorylation site in human 53BP1 kinase (see Row 252 in Table 1 (SEQ ID NO: 251)), is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer (see Merrifield, supra.) as further described below in Synthesis & MS/MS Signature. The 53BP1 (ser105) AQUA peptide is then spiked into a biological sample to quantify the amount of phosphorylated 53BP1 (ser 105) in the sample, as further described below in Analysis & Quantification.

C. PSF2 (Serine 182)

An AQUA peptide comprising the sequence, TNLQPLESTQs*QDF (y*=phosphoserine; sequence incorporating ¹⁴C/¹⁵N-labeled phenylalanine (indicated by bold F), which corresponds to the serine 182 phosphorylation site in human PSF2 DNA replication protein (see Row 108 in Table 1 (SEQ ID NO: 107)), is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer (see Merrifield, supra.) as further described below in Synthesis & MS/MS Signature. The PSF2 (ser182) AQUA peptide is then spiked into a biological sample to quantify the amount of phosphorylated PSF2 (ser 82) in the sample, as further described below in Analysis & Quantification.

D. FOXJ2 (Serine 161).

An AQUA peptide comprising the sequence, RHPPDDDLs*QDSPEQEASKSPR (s*=phosphoserine; sequence incorporating ¹⁴C/¹⁵N-labeled proline (indicated by bold P), which corresponds to the serine 161 phosphorylation site in human FOXJ2 protein (see Row 225 in Table 1 (SEQ ID NO: 224)), is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer (see Merrifield, supra.) as further described below in Synthesis & MS/MS Signature. The FOXJ2 (ser161) AQUA peptide is then spiked into a biological sample to quantify the amount of phosphorylated FOXJ2 (ser161) in the sample, as further described below in Analysis & Quantification.

Synthesis & MS/MS Spectra.

Fluorenylmethoxycarbonyl (Fmoc)-derivatized amino acid monomers may be obtained from AnaSpec (San Jose, Calif.). Fmoc-derivatized stable-isotope monomers containing one ¹⁵N and five to nine ¹³C atoms may be obtained from Cambridge Isotope Laboratories (Andover, Mass.). Preloaded Wang resins may be obtained from Applied Biosystems. Synthesis scales may vary from 5 to 25 μmol. Amino acids are activated in situ with 1-H-benzotriazolium, 1-bis(dimethylamino)methylene]-hexafluorophosphate (1-),3-oxide:1-hydroxybenzotriazole hydrate and coupled at a 5-fold molar excess over peptide. Each coupling cycle is followed by capping with acetic anhydride to avoid accumulation of one-residue deletion peptide by-products. After synthesis peptide-resins are treated with a standard scavenger-containing trifluoroacetic acid (TFA)-water cleavage solution, and the peptides are precipitated by addition to cold ether. Peptides (i.e. a desired AQUA peptide described in A-D above) are purified by reversed-phase C18 HPLC using standard TFA/acetonitrile gradients and characterized by matrix-assisted laser desorption ionization-time of flight (Biflex III, Bruker Daltonics, Billerica, Mass.) and ion-trap (ThermoFinnigan, LCQ DecaXP) MS.

MS/MS spectra for each AQUA peptide should exhibit a strong y-type ion peak as the most intense fragment ion that is suitable for use in an SRM monitoring/analysis. Reverse-phase microcapillary columns (0.1 Å˜150-220 mm) are prepared according to standard methods. An Agilent 1100 liquid chromatograph may be used to develop and deliver a solvent gradient [0.4% acetic acid/0.005% heptafluorobutyric acid (HFBA)/7% methanol and 0.4% acetic acid/0.005% HFBA/65% methanol/35% acetonitrile] to the microcapillary column by means of a flow splitter. Samples are then directly loaded onto the microcapillary column by using a FAMOS inert capillary autosampler (LC Packings, San Francisco) after the flow split. Peptides are reconstituted in 6% acetic acid/0.01% TFA before injection.

Analysis & Quantification.

Target protein (e.g. a phosphorylated protein of A-D above) in a biological sample is quantified using a validated AQUA peptide (as described above). The IAP method is then applied to the complex mixture of peptides derived from proteolytic cleavage of crude cell extracts to which the AQUA peptides have been spiked in.

LC-SRM of the entire sample is then carried out. MS/MS may be performed by using a ThermoFinnigan (San Jose, Calif.) mass spectrometer (LCQ DecaXP ion trap or TSQ Quantum triple quadrupole). On the DecaXP, parent ions are isolated at 1.6 m/z width, the ion injection time being limited to 150 ms per microscan, with two microscans per peptide averaged, and with an AGC setting of 1×10⁸; on the Quantum, Q1 is kept at 0.4 and Q3 at 0.8 m/z with a scan time of 200 ms per peptide. On both instruments, analyte and internal standard are analyzed in alternation within a previously known reverse-phase retention window; well-resolved pairs of internal standard and analyte are analyzed in separate retention segments to improve duty cycle. Data are processed by integrating the appropriate peaks in an extracted ion chromatogram (60.15 m/z from the fragment monitored) for the native and internal standard, followed by calculation of the ratio of peak areas multiplied by the absolute amount of internal standard (e.g., 500 fmol). 

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 53. An isolated phosphorylation site-specific antibody that specifically binds a human ATM and/or ATR kinase signaling protein selected from Column A of Table 1, Rows 70, 173, 176, 243 and 259 only when phosphorylated at the serine or threonine listed in corresponding Column D of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E of Table 1 (SEQ ID NOs: 69, 172, 175, 242 and 258), wherein said antibody does not bind said signaling protein when not phosphorylated at said serine or threonine.
 54. An isolated phosphorylation site-specific antibody that specifically binds a human ATM and/or ATR kinase signaling protein selected from Column A of Table 1, Rows 70, 173, 176, 243 and 259 only when not phosphorylated at the serine or threonine listed in corresponding Column D of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E of Table 1 (SEQ ID NOs: 69, 172, 175, 242 and 258), wherein said antibody does not bind said signaling protein when phosphorylated at said serine or threonine.
 55. A method selected from the group consisting of: (a) a method for detecting a human ATM and/or ATR kinase signaling protein selected from Column A of Table 1, Rows 70, 173, 176, 243 and 259 wherein said human ATM and/or ATR kinase signaling protein is phosphorylated at the serine or threonine listed in corresponding Column D of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E of Table 1 (SEQ ID NOs: 69, 172, 175, 242 and 258), comprising the step of adding an isolated phosphorylation-specific antibody according to claim 53, to a sample comprising said human ATM and/or ATR kinase signaling protein under conditions that permit the binding of said antibody to said human ATM and/or ATR kinase signaling protein, and detecting bound antibody; (b) a method for quantifying the amount of a human ATM and/or ATR kinase signaling protein listed in Column A of Table 1, Rows 70, 173, 176, 243 and 259 that is phosphorylated at the corresponding serine or threonine listed in Column D of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E of Table 1 (SEQ ID NOs: 69, 172, 175, 242 and 258), in a sample using a heavy-isotope labeled peptide (AQUA™ peptide), said labeled peptide comprising a phosphorylated serine or threonine at said corresponding serine or threonine listed Column D of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E of Table 1 as an internal standard; and (c) a method comprising step (a) followed by step (b).
 56. The method of claim 55, wherein said isolated phosphorylation-specific antibody is capable of specifically binding 53BP1 only when phosphorylated at T855, comprised within the phosphorylatable peptide sequence listed in Column E, Row 243, of Table 1 (SEQ ID NO: 242), wherein said antibody does not bind said protein when not phosphorylated at said threonine.
 57. The method of claim 55, wherein said isolated phosphorylation-specific antibody is capable of specifically binding 53BP1 only when not phosphorylated at T855, comprised within the phosphorylatable peptide sequence listed in Column E, Row 243, of Table 1 (SEQ ID NO: 242), wherein said antibody does not bind said protein when phosphorylated at said threonine.
 58. The method of claim 55, wherein said isolated phosphorylation-specific antibody is capable of specifically binding MYST2 only when phosphorylated at S53, comprised within the phosphorylatable peptide sequence listed in Column E, Row 259, of Table 1 (SEQ ID NO: 258), wherein said antibody does not bind said protein when not phosphorylated at said serine.
 59. The method of claim 55, wherein said isolated phosphorylation-specific antibody is capable of specifically binding MYST2 only when not phosphorylated at S53, comprised within the phosphorylatable peptide sequence listed in Column E, Row 259, of Table 1 (SEQ ID NO: 258), wherein said antibody does not bind said protein when phosphorylated at said serine.
 60. The method of claim 55, wherein said isolated phosphorylation-specific antibody is capable of specifically binding SMG1 only when phosphorylated at S3556, comprised within the phosphorylatable peptide sequence listed in Column E, Row 176, of Table 1 (SEQ ID NO: 175), wherein said antibody does not bind said protein when not phosphorylated at said serine.
 61. The method of claim 55, wherein said isolated phosphorylation-specific antibody is capable of specifically binding SMG1 only when not phosphorylated at S3556, comprised within the phosphorylatable peptide sequence listed in Column E, Row 176, of Table 1 (SEQ ID NO: 175), wherein said antibody does not bind said protein when phosphorylated at said serine.
 62. The method of claim 55, wherein said isolated phosphorylation-specific antibody is capable of specifically binding ARID1A only when phosphorylated at S604, comprised within the phosphorylatable peptide sequence listed in Column E, Row 70, of Table 1 (SEQ ID NO: 69), wherein said antibody does not bind said protein when not phosphorylated at said serine.
 63. The method of claim 55, wherein said isolated phosphorylation-specific antibody is capable of specifically binding AIRD1A only when not phosphorylated at S604, comprised within the phosphorylatable peptide sequence listed in Column E, Row 70, of Table 1 (SEQ ID NO: 69), wherein said antibody does not bind said protein when phosphorylated at said serine.
 64. The method of claim 55, wherein said isolated phosphorylation-specific antibody is capable of specifically binding NLK only when phosphorylated at T286, comprised within the phosphorylatable peptide sequence listed in Column E, Row 173, of Table 1 (SEQ ID NO: 172), wherein said antibody does not bind said protein when not phosphorylated at said serine.
 65. The method of claim 55, wherein said isolated phosphorylation-specific antibody is capable of specifically binding NLK only when not phosphorylated at T286, comprised within the phosphorylatable peptide sequence listed in Column E, Row 173, of Table 1 (SEQ ID NO: 172), wherein said antibody does not bind said protein when phosphorylated at said serine. 